RNA velocity using Bioconductor
Frederick J Tan
27 March 2021
Load package directory
.libPaths( "/home/idies/workspace/c_moor_data/R/4.0.3/osca/" )
.libPaths()[1] "/home/idies/workspace/c_moor_data/R/4.0.3/osca"
[2] "/home/idies/R/lib64/R/library" Load data
library( "scRNAseq" )Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet,
colCollapse, colCounts, colCummaxs, colCummins,
colCumprods, colCumsums, colDiffs, colIQRDiffs,
colIQRs, colLogSumExps, colMadDiffs, colMads,
colMaxs, colMeans2, colMedians, colMins,
colOrderStats, colProds, colQuantiles, colRanges,
colRanks, colSdDiffs, colSds, colSums2,
colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians,
colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs,
rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts,
rowCummaxs, rowCummins, rowCumprods, rowCumsums,
rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2,
rowMedians, rowMins, rowOrderStats, rowProds,
rowQuantiles, rowRanges, rowRanks, rowSdDiffs,
rowSds, rowSums2, rowTabulates, rowVarDiffs,
rowVars, rowWeightedMads, rowWeightedMeans,
rowWeightedMedians, rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
Registered S3 methods overwritten by 'dbplyr':
method from
print.tbl_lazy
print.tbl_sql sce.sperm <- HermannSpermatogenesisData( strip=TRUE, location=TRUE )
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|=======================================================================| 100%snapshotDate(): 2020-10-27
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
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|=======================================================================| 100%loading from cache
require("ensembldb")Quality control
library( "scuttle" )
is.mito <- which( seqnames(sce.sperm)=="MT" )
sce.sperm <- addPerCellQC(
sce.sperm, subsets=list(Mt=is.mito), assay.type="spliced"
)Warning: call dbDisconnect() when finished working with a connectionqc <- quickPerCellQC( colData(sce.sperm), sub.fields=TRUE )
sce.sperm <- sce.sperm[,!qc$discard]Normalization
library( "scran" )
sce.sperm <- logNormCounts( sce.sperm, assay.type="spliced" )
dec <- modelGeneVarByPoisson( sce.sperm, assay.type="spliced" )
hvgs <- getTopHVGs( dec, n=2500 )Dimensionality reduction
library( "scater" )Loading required package: ggplot2sce.sperm <- runPCA( sce.sperm, ncomponents=25, subset_row=hvgs )
sce.sperm <- runTSNE( sce.sperm, dimred="PCA" )RNA velocity
library( "velociraptor" )
velo.out <- scvelo(
sce.sperm, assay.X="spliced",
subset.row=hvgs, use.dimred="PCA"
)adding rname 'https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.3-Linux-x86_64.sh'
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PREFIX=/home/idies/.cache/basilisk/1.2.1/0
Unpacking payload ...
0%| | 0/35 [00:00<?, ?it/s]
Extracting : libffi-3.3-he6710b0_1.conda: 0%| | 0/35 [00:00<?, ?it/s]
Extracting : libffi-3.3-he6710b0_1.conda: 3%|▎ | 1/35 [00:00<00:10, 3.25it/s]
Extracting : ruamel_yaml-0.15.87-py37h7b6447c_0.conda: 3%|▎ | 1/35 [00:00<00:10, 3.25it/s]
Extracting : ruamel_yaml-0.15.87-py37h7b6447c_0.conda: 6%|▌ | 2/35 [00:00<00:09, 3.31it/s]
Extracting : pycosat-0.6.3-py37h7b6447c_0.conda: 6%|▌ | 2/35 [00:00<00:09, 3.31it/s]
Extracting : ncurses-6.2-he6710b0_1.conda: 9%|▊ | 3/35 [00:04<00:09, 3.31it/s]
Extracting : ncurses-6.2-he6710b0_1.conda: 11%|█▏ | 4/35 [00:04<00:24, 1.24it/s]
Extracting : openssl-1.1.1g-h7b6447c_0.conda: 11%|█▏ | 4/35 [00:04<00:24, 1.24it/s]
Extracting : cryptography-2.9.2-py37h1ba5d50_0.conda: 14%|█▍ | 5/35 [00:04<00:24, 1.24it/s]
Extracting : chardet-3.0.4-py37_1003.conda: 17%|█▋ | 6/35 [00:04<00:23, 1.24it/s]
Extracting : conda-package-handling-1.6.1-py37h7b6447c_0.conda: 20%|██ | 7/35 [00:04<00:22, 1.24it/s]
Extracting : pysocks-1.7.1-py37_0.conda: 23%|██▎ | 8/35 [00:04<00:21, 1.24it/s]
Extracting : idna-2.9-py_1.conda: 26%|██▌ | 9/35 [00:04<00:20, 1.24it/s]
Extracting : urllib3-1.25.8-py37_0.conda: 29%|██▊ | 10/35 [00:04<00:20, 1.24it/s]
Extracting : six-1.14.0-py37_0.conda: 31%|███▏ | 11/35 [00:04<00:19, 1.24it/s]
Extracting : libgcc-ng-9.1.0-hdf63c60_0.conda: 34%|███▍ | 12/35 [00:04<00:18, 1.24it/s]
Extracting : sqlite-3.31.1-h62c20be_1.conda: 37%|███▋ | 13/35 [00:04<00:17, 1.24it/s]
Extracting : yaml-0.1.7-had09818_2.conda: 40%|████ | 14/35 [00:04<00:16, 1.24it/s]
Extracting : _libgcc_mutex-0.1-main.conda: 43%|████▎ | 15/35 [00:04<00:16, 1.24it/s]
Extracting : pycparser-2.20-py_0.conda: 46%|████▌ | 16/35 [00:04<00:15, 1.24it/s]
Extracting : ca-certificates-2020.1.1-0.conda: 49%|████▊ | 17/35 [00:04<00:14, 1.24it/s]
Extracting : readline-8.0-h7b6447c_0.conda: 51%|█████▏ | 18/35 [00:04<00:13, 1.24it/s]
Extracting : pip-20.0.2-py37_3.conda: 54%|█████▍ | 19/35 [00:04<00:12, 1.24it/s]
Extracting : python-3.7.7-hcff3b4d_5.conda: 57%|█████▋ | 20/35 [00:05<00:12, 1.24it/s]
Extracting : python-3.7.7-hcff3b4d_5.conda: 60%|██████ | 21/35 [00:05<00:08, 1.72it/s]
Extracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda: 60%|██████ | 21/35 [00:05<00:08, 1.72it/s]
Extracting : wheel-0.34.2-py37_0.conda: 63%|██████▎ | 22/35 [00:05<00:07, 1.72it/s]
Extracting : libedit-3.1.20181209-hc058e9b_0.conda: 66%|██████▌ | 23/35 [00:05<00:06, 1.72it/s]
Extracting : tqdm-4.46.0-py_0.conda: 69%|██████▊ | 24/35 [00:05<00:06, 1.72it/s]
Extracting : zlib-1.2.11-h7b6447c_3.conda: 71%|███████▏ | 25/35 [00:05<00:05, 1.72it/s]
Extracting : certifi-2020.4.5.1-py37_0.conda: 74%|███████▍ | 26/35 [00:05<00:05, 1.72it/s]
Extracting : setuptools-46.4.0-py37_0.conda: 77%|███████▋ | 27/35 [00:05<00:04, 1.72it/s]
Extracting : ld_impl_linux-64-2.33.1-h53a641e_7.conda: 80%|████████ | 28/35 [00:05<00:04, 1.72it/s]
Extracting : requests-2.23.0-py37_0.conda: 83%|████████▎ | 29/35 [00:05<00:03, 1.72it/s]
Extracting : tk-8.6.8-hbc83047_0.conda: 86%|████████▌ | 30/35 [00:05<00:02, 1.72it/s]
Extracting : cffi-1.14.0-py37he30daa8_1.conda: 89%|████████▊ | 31/35 [00:05<00:02, 1.72it/s]
Extracting : pyopenssl-19.1.0-py37_0.conda: 91%|█████████▏| 32/35 [00:05<00:01, 1.72it/s]
Extracting : xz-5.2.5-h7b6447c_0.conda: 94%|█████████▍| 33/35 [00:05<00:01, 1.72it/s]
Extracting : conda-4.8.3-py37_0.tar.bz2: 97%|█████████▋| 34/35 [00:05<00:00, 1.72it/s]
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/idies/.cache/basilisk/1.2.1/0
added / updated specs:
- _libgcc_mutex==0.1=main
- ca-certificates==2020.1.1=0
- certifi==2020.4.5.1=py37_0
- cffi==1.14.0=py37he30daa8_1
- chardet==3.0.4=py37_1003
- conda-package-handling==1.6.1=py37h7b6447c_0
- conda==4.8.3=py37_0
- cryptography==2.9.2=py37h1ba5d50_0
- idna==2.9=py_1
- ld_impl_linux-64==2.33.1=h53a641e_7
- libedit==3.1.20181209=hc058e9b_0
- libffi==3.3=he6710b0_1
- libgcc-ng==9.1.0=hdf63c60_0
- libstdcxx-ng==9.1.0=hdf63c60_0
- ncurses==6.2=he6710b0_1
- openssl==1.1.1g=h7b6447c_0
- pip==20.0.2=py37_3
- pycosat==0.6.3=py37h7b6447c_0
- pycparser==2.20=py_0
- pyopenssl==19.1.0=py37_0
- pysocks==1.7.1=py37_0
- python==3.7.7=hcff3b4d_5
- readline==8.0=h7b6447c_0
- requests==2.23.0=py37_0
- ruamel_yaml==0.15.87=py37h7b6447c_0
- setuptools==46.4.0=py37_0
- six==1.14.0=py37_0
- sqlite==3.31.1=h62c20be_1
- tk==8.6.8=hbc83047_0
- tqdm==4.46.0=py_0
- urllib3==1.25.8=py37_0
- wheel==0.34.2=py37_0
- xz==5.2.5=h7b6447c_0
- yaml==0.1.7=had09818_2
- zlib==1.2.11=h7b6447c_3
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
ca-certificates pkgs/main/linux-64::ca-certificates-2020.1.1-0
certifi pkgs/main/linux-64::certifi-2020.4.5.1-py37_0
cffi pkgs/main/linux-64::cffi-1.14.0-py37he30daa8_1
chardet pkgs/main/linux-64::chardet-3.0.4-py37_1003
conda pkgs/main/linux-64::conda-4.8.3-py37_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.1-py37h7b6447c_0
cryptography pkgs/main/linux-64::cryptography-2.9.2-py37h1ba5d50_0
idna pkgs/main/noarch::idna-2.9-py_1
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_1
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1
openssl pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0
pip pkgs/main/linux-64::pip-20.0.2-py37_3
pycosat pkgs/main/linux-64::pycosat-0.6.3-py37h7b6447c_0
pycparser pkgs/main/noarch::pycparser-2.20-py_0
pyopenssl pkgs/main/linux-64::pyopenssl-19.1.0-py37_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py37_0
python pkgs/main/linux-64::python-3.7.7-hcff3b4d_5
readline pkgs/main/linux-64::readline-8.0-h7b6447c_0
requests pkgs/main/linux-64::requests-2.23.0-py37_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py37h7b6447c_0
setuptools pkgs/main/linux-64::setuptools-46.4.0-py37_0
six pkgs/main/linux-64::six-1.14.0-py37_0
sqlite pkgs/main/linux-64::sqlite-3.31.1-h62c20be_1
tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0
tqdm pkgs/main/noarch::tqdm-4.46.0-py_0
urllib3 pkgs/main/linux-64::urllib3-1.25.8-py37_0
wheel pkgs/main/linux-64::wheel-0.34.2-py37_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.1.7-had09818_2
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
Preparing transaction: ...working... done
Executing transaction: ...working... done
installation finished.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/idies/.cache/basilisk/1.2.1/velociraptor-1.0.0/env
added / updated specs:
- python=3.7.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | conda_forge 3 KB conda-forge
_openmp_mutex-4.5 | 1_gnu 22 KB conda-forge
ca-certificates-2020.12.5 | ha878542_0 137 KB conda-forge
certifi-2020.12.5 | py37h89c1867_1 143 KB conda-forge
ld_impl_linux-64-2.35.1 | hea4e1c9_2 618 KB conda-forge
libffi-3.3 | h58526e2_2 51 KB conda-forge
libgcc-ng-9.3.0 | h2828fa1_18 7.8 MB conda-forge
libgomp-9.3.0 | h2828fa1_18 376 KB conda-forge
libstdcxx-ng-9.3.0 | h6de172a_18 4.0 MB conda-forge
ncurses-6.2 | h58526e2_4 985 KB conda-forge
openssl-1.1.1k | h7f98852_0 2.1 MB conda-forge
pip-21.0.1 | pyhd8ed1ab_0 1.1 MB conda-forge
python_abi-3.7 | 1_cp37m 4 KB conda-forge
readline-8.0 | he28a2e2_2 281 KB conda-forge
setuptools-49.6.0 | py37h89c1867_3 947 KB conda-forge
sqlite-3.35.3 | h74cdb3f_0 1.4 MB conda-forge
tk-8.6.10 | h21135ba_1 3.2 MB conda-forge
wheel-0.36.2 | pyhd3deb0d_0 31 KB conda-forge
xz-5.2.5 | h516909a_1 343 KB conda-forge
zlib-1.2.11 | h516909a_1010 106 KB conda-forge
------------------------------------------------------------
Total: 23.6 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0
certifi conda-forge/linux-64::certifi-2020.12.5-py37h89c1867_1
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_2
libffi conda-forge/linux-64::libffi-3.3-h58526e2_2
libgcc-ng conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_18
libgomp conda-forge/linux-64::libgomp-9.3.0-h2828fa1_18
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_18
ncurses conda-forge/linux-64::ncurses-6.2-h58526e2_4
openssl conda-forge/linux-64::openssl-1.1.1k-h7f98852_0
pip conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
python pkgs/main/linux-64::python-3.7.7-hcff3b4d_5
python_abi conda-forge/linux-64::python_abi-3.7-1_cp37m
readline conda-forge/linux-64::readline-8.0-he28a2e2_2
setuptools conda-forge/linux-64::setuptools-49.6.0-py37h89c1867_3
sqlite conda-forge/linux-64::sqlite-3.35.3-h74cdb3f_0
tk conda-forge/linux-64::tk-8.6.10-h21135ba_1
wheel conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
xz conda-forge/linux-64::xz-5.2.5-h516909a_1
zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1010
Downloading and Extracting Packages
xz-5.2.5 | 343 KB | | 0%
xz-5.2.5 | 343 KB | 4 | 5%
xz-5.2.5 | 343 KB | ########## | 100%
libgcc-ng-9.3.0 | 7.8 MB | | 0%
libgcc-ng-9.3.0 | 7.8 MB | ##3 | 24%
libgcc-ng-9.3.0 | 7.8 MB | #####2 | 53%
libgcc-ng-9.3.0 | 7.8 MB | ########## | 100%
wheel-0.36.2 | 31 KB | | 0%
wheel-0.36.2 | 31 KB | ########## | 100%
zlib-1.2.11 | 106 KB | | 0%
zlib-1.2.11 | 106 KB | ########## | 100%
ld_impl_linux-64-2.3 | 618 KB | | 0%
ld_impl_linux-64-2.3 | 618 KB | ########## | 100%
libgomp-9.3.0 | 376 KB | | 0%
libgomp-9.3.0 | 376 KB | ########## | 100%
_openmp_mutex-4.5 | 22 KB | | 0%
_openmp_mutex-4.5 | 22 KB | ########## | 100%
sqlite-3.35.3 | 1.4 MB | | 0%
sqlite-3.35.3 | 1.4 MB | ########## | 100%
readline-8.0 | 281 KB | | 0%
readline-8.0 | 281 KB | ########## | 100%
openssl-1.1.1k | 2.1 MB | | 0%
openssl-1.1.1k | 2.1 MB | ########## | 100%
python_abi-3.7 | 4 KB | | 0%
python_abi-3.7 | 4 KB | ########## | 100%
libffi-3.3 | 51 KB | | 0%
libffi-3.3 | 51 KB | ########## | 100%
ncurses-6.2 | 985 KB | | 0%
ncurses-6.2 | 985 KB | ########## | 100%
certifi-2020.12.5 | 143 KB | | 0%
certifi-2020.12.5 | 143 KB | ########## | 100%
setuptools-49.6.0 | 947 KB | | 0%
setuptools-49.6.0 | 947 KB | ########## | 100%
tk-8.6.10 | 3.2 MB | | 0%
tk-8.6.10 | 3.2 MB | #######3 | 74%
tk-8.6.10 | 3.2 MB | ########## | 100%
_libgcc_mutex-0.1 | 3 KB | | 0%
_libgcc_mutex-0.1 | 3 KB | ########## | 100%
ca-certificates-2020 | 137 KB | | 0%
ca-certificates-2020 | 137 KB | ########## | 100%
pip-21.0.1 | 1.1 MB | | 0%
pip-21.0.1 | 1.1 MB | ########## | 100%
libstdcxx-ng-9.3.0 | 4.0 MB | | 0%
libstdcxx-ng-9.3.0 | 4.0 MB | ######3 | 63%
libstdcxx-ng-9.3.0 | 4.0 MB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
# $ conda activate /home/idies/.cache/basilisk/1.2.1/velociraptor-1.0.0/env
#
# To deactivate an active environment, use
#
# $ conda deactivate
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.9.2
Please update conda by running
$ conda update -n base -c defaults condaCollecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/idies/.cache/basilisk/1.2.1/velociraptor-1.0.0/env
added / updated specs:
- python=3.7.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2021.1.19 | h06a4308_1 118 KB
certifi-2020.12.5 | py37h06a4308_0 141 KB
openssl-1.1.1k | h27cfd23_0 2.5 MB
------------------------------------------------------------
Total: 2.8 MB
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2020.12.~ --> pkgs/main::ca-certificates-2021.1.19-h06a4308_1
The following packages will be SUPERSEDED by a higher-priority channel:
certifi conda-forge::certifi-2020.12.5-py37h8~ --> pkgs/main::certifi-2020.12.5-py37h06a4308_0
openssl conda-forge::openssl-1.1.1k-h7f98852_0 --> pkgs/main::openssl-1.1.1k-h27cfd23_0
Downloading and Extracting Packages
certifi-2020.12.5 | 141 KB | | 0%
certifi-2020.12.5 | 141 KB | #1 | 11%
certifi-2020.12.5 | 141 KB | ########## | 100%
openssl-1.1.1k | 2.5 MB | | 0%
openssl-1.1.1k | 2.5 MB | ########## | 100%
ca-certificates-2021 | 118 KB | | 0%
ca-certificates-2021 | 118 KB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.9.2
Please update conda by running
$ conda update -n base -c defaults condaCollecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/idies/.cache/basilisk/1.2.1/velociraptor-1.0.0/env
added / updated specs:
- alabaster=0.7.12
- anndata=0.7.4
- babel=2.8.0
- brotlipy=0.7.0
- certifi=2020.6.20
- cffi=1.14.1
- chardet=3.0.4
- colorama=0.4.3
- cryptography=3.1
- cycler=0.10.0
- decorator=4.4.2
- docutils=0.16
- h5py=2.10.0
- idna=2.10
- imagesize=1.2.0
- importlib-metadata=1.7.0
- jinja2=2.11.2
- joblib=0.16.0
- kiwisolver=1.2.0
- llvmlite=0.34.0
- loompy=2.0.16
- markupsafe=1.1.1
- matplotlib=3.3.1
- mock=4.0.2
- natsort=7.0.1
- networkx=2.5
- numba=0.51.2
- numexpr=2.7.1
- numpy=1.19.1
- olefile=0.46
- packaging=20.4
- pandas=1.1.2
- patsy=0.5.1
- pillow=7.2.0
- pip=20.2.3
- pycparser=2.20
- pygments=2.7.0
- pyopenssl=19.1.0
- pyparsing=2.4.7
- pysocks=1.7.1
- python-dateutil=2.8.1
- python=3.7.7
- pytz=2020.1
- requests=2.24.0
- scanpy=1.6.0
- scikit-learn=0.23.2
- scipy=1.5.2
- scvelo=0.2.2
- seaborn=0.11.0
- setuptools-scm=4.1.2
- sinfo=0.3.1
- six=1.15.0
- snowballstemmer=2.0.0
- sphinx=3.2.1
- sphinxcontrib-applehelp=1.0.2
- sphinxcontrib-devhelp=1.0.2
- sphinxcontrib-htmlhelp=1.0.3
- sphinxcontrib-jsmath=1.0.1
- sphinxcontrib-qthelp=1.0.3
- sphinxcontrib-serializinghtml=1.1.4
- statsmodels=0.12.0
- stdlib-list=0.6.0
- threadpoolctl=2.1.0
- toml=0.10.1
- tornado=6.0.4
- tqdm=4.49.0
- umap-learn=0.4.6
- urllib3=1.25.10
- wheel=0.35.1
- zipp=3.1.0
The following packages will be downloaded:
package | build
---------------------------|-----------------
alabaster-0.7.12 | py_0 15 KB conda-forge
anndata-0.7.4 | py37h89c1867_1 187 KB conda-forge
babel-2.8.0 | py_0 6.0 MB conda-forge
blosc-1.21.0 | h9c3ff4c_0 841 KB conda-forge
brotlipy-0.7.0 |py37h5e8e339_1001 341 KB conda-forge
bzip2-1.0.8 | h7f98852_4 484 KB conda-forge
certifi-2020.6.20 | py37he5f6b98_2 151 KB conda-forge
cffi-1.14.1 | py37he30daa8_0 226 KB
chardet-3.0.4 |py37he5f6b98_1008 170 KB conda-forge
colorama-0.4.3 | py_0 17 KB conda-forge
cryptography-3.1.1 | py37hff6837a_1 616 KB conda-forge
cycler-0.10.0 | py_2 9 KB conda-forge
decorator-4.4.2 | py_0 11 KB conda-forge
docutils-0.16 | py37h89c1867_3 739 KB conda-forge
freetype-2.10.4 | h0708190_1 890 KB conda-forge
get_version-2.1 | py_1 21 KB conda-forge
h5py-2.10.0 |nompi_py37hf7afa78_105 1.1 MB conda-forge
hdf5-1.10.6 |nompi_h6a2412b_1114 3.1 MB conda-forge
idna-2.10 | pyh9f0ad1d_0 52 KB conda-forge
imagesize-1.2.0 | py_0 8 KB conda-forge
importlib-metadata-1.7.0 | pyhd8ed1ab_1 28 KB conda-forge
importlib_metadata-1.7.0 | hd8ed1ab_1 3 KB conda-forge
jinja2-2.11.2 | pyh9f0ad1d_0 93 KB conda-forge
joblib-0.16.0 | py_0 203 KB conda-forge
jpeg-9d | h36c2ea0_0 264 KB conda-forge
kiwisolver-1.2.0 | py37h99015e2_1 88 KB conda-forge
krb5-1.17.2 | h926e7f8_0 1.4 MB conda-forge
lcms2-2.12 | hddcbb42_0 443 KB conda-forge
legacy-api-wrap-1.2 | py_0 18 KB conda-forge
libblas-3.9.0 | 8_openblas 11 KB conda-forge
libcblas-3.9.0 | 8_openblas 11 KB conda-forge
libcurl-7.71.1 | hcdd3856_3 302 KB conda-forge
libedit-3.1.20191231 | he28a2e2_2 121 KB conda-forge
libgfortran-ng-9.3.0 | hff62375_18 22 KB conda-forge
libgfortran5-9.3.0 | hff62375_18 2.0 MB conda-forge
liblapack-3.9.0 | 8_openblas 11 KB conda-forge
libllvm10-10.0.1 | he513fc3_3 26.4 MB conda-forge
libopenblas-0.3.12 |pthreads_h4812303_1 8.9 MB conda-forge
libpng-1.6.37 | h21135ba_2 306 KB conda-forge
libssh2-1.9.0 | ha56f1ee_6 226 KB conda-forge
libtiff-4.2.0 | hdc55705_0 633 KB conda-forge
libwebp-base-1.2.0 | h7f98852_2 815 KB conda-forge
llvmlite-0.34.0 | py37h5202443_2 322 KB conda-forge
loompy-2.0.16 | py_0 31 KB bioconda
lz4-c-1.9.3 | h9c3ff4c_0 179 KB conda-forge
lzo-2.10 | h516909a_1000 314 KB conda-forge
markupsafe-1.1.1 | py37h5e8e339_3 27 KB conda-forge
matplotlib-3.3.1 | 1 6 KB conda-forge
matplotlib-base-3.3.1 | py37hd478181_1 6.7 MB conda-forge
mock-4.0.2 | py37hc8dfbb8_1 51 KB conda-forge
natsort-7.0.1 | py_0 32 KB conda-forge
networkx-2.5 | py_0 1.2 MB conda-forge
numba-0.51.2 | py37h9fdb41a_0 3.6 MB conda-forge
numexpr-2.7.1 | py37h9fdb41a_3 197 KB conda-forge
numpy-1.19.1 | py37h7ea13bd_2 5.2 MB conda-forge
olefile-0.46 | pyh9f0ad1d_1 32 KB conda-forge
packaging-20.4 | pyh9f0ad1d_0 32 KB conda-forge
pandas-1.1.2 | py37h3340039_0 10.5 MB conda-forge
patsy-0.5.1 | py_0 187 KB conda-forge
pillow-7.2.0 | py37h718be6c_2 671 KB conda-forge
pip-20.2.3 | py_0 1.1 MB conda-forge
pycparser-2.20 | pyh9f0ad1d_2 94 KB conda-forge
pygments-2.7.0 | py_0 706 KB conda-forge
pyopenssl-19.1.0 | py_1 47 KB conda-forge
pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB conda-forge
pysocks-1.7.1 | py37h89c1867_3 27 KB conda-forge
pytables-3.6.1 | py37h0c4f3e0_3 1.5 MB conda-forge
python-dateutil-2.8.1 | py_0 220 KB conda-forge
pytz-2020.1 | pyh9f0ad1d_0 227 KB conda-forge
requests-2.24.0 | pyh9f0ad1d_0 47 KB conda-forge
scanpy-1.6.0 | py_1 7.1 MB bioconda
scikit-learn-0.23.2 | py37hddcf8d6_3 6.8 MB conda-forge
scipy-1.5.2 | py37h14a347d_2 19.0 MB conda-forge
scvelo-0.2.2 | py_1 145 KB bioconda
seaborn-0.11.0 | ha770c72_1 4 KB conda-forge
seaborn-base-0.11.0 | pyhd8ed1ab_1 216 KB conda-forge
setuptools-scm-4.1.2 | pyh9f0ad1d_0 25 KB conda-forge
setuptools_scm-4.1.2 | 0 3 KB conda-forge
sinfo-0.3.1 | py_0 11 KB conda-forge
six-1.15.0 | pyh9f0ad1d_0 14 KB conda-forge
snowballstemmer-2.0.0 | py_0 55 KB conda-forge
sphinx-3.2.1 | py_0 1.4 MB conda-forge
sphinxcontrib-applehelp-1.0.2| py_0 28 KB conda-forge
sphinxcontrib-devhelp-1.0.2| py_0 22 KB conda-forge
sphinxcontrib-htmlhelp-1.0.3| py_0 27 KB conda-forge
sphinxcontrib-jsmath-1.0.1 | py_0 7 KB conda-forge
sphinxcontrib-qthelp-1.0.3 | py_0 25 KB conda-forge
sphinxcontrib-serializinghtml-1.1.4| py_0 24 KB conda-forge
statsmodels-0.12.0 | py37h161383b_1 11.0 MB conda-forge
stdlib-list-0.6.0 | py37_0 16 KB conda-forge
tbb-2020.2 | h4bd325d_4 1.5 MB conda-forge
threadpoolctl-2.1.0 | pyh5ca1d4c_0 15 KB conda-forge
toml-0.10.1 | pyh9f0ad1d_0 18 KB conda-forge
tornado-6.0.4 | py37h8f50634_2 641 KB conda-forge
tqdm-4.49.0 | pyh9f0ad1d_0 54 KB conda-forge
typing-3.7.4.3 | pyhd8ed1ab_2 7 KB conda-forge
umap-learn-0.4.6 | py37hc8dfbb8_0 110 KB conda-forge
urllib3-1.25.10 | py_0 92 KB conda-forge
wheel-0.35.1 | pyh9f0ad1d_0 29 KB conda-forge
zipp-3.1.0 | py_0 10 KB conda-forge
zstd-1.4.9 | ha95c52a_0 431 KB conda-forge
------------------------------------------------------------
Total: 139.1 MB
The following NEW packages will be INSTALLED:
alabaster conda-forge/noarch::alabaster-0.7.12-py_0
anndata conda-forge/linux-64::anndata-0.7.4-py37h89c1867_1
babel conda-forge/noarch::babel-2.8.0-py_0
blosc conda-forge/linux-64::blosc-1.21.0-h9c3ff4c_0
brotlipy conda-forge/linux-64::brotlipy-0.7.0-py37h5e8e339_1001
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
cffi pkgs/main/linux-64::cffi-1.14.1-py37he30daa8_0
chardet conda-forge/linux-64::chardet-3.0.4-py37he5f6b98_1008
colorama conda-forge/noarch::colorama-0.4.3-py_0
cryptography conda-forge/linux-64::cryptography-3.1.1-py37hff6837a_1
cycler conda-forge/noarch::cycler-0.10.0-py_2
decorator conda-forge/noarch::decorator-4.4.2-py_0
docutils conda-forge/linux-64::docutils-0.16-py37h89c1867_3
freetype conda-forge/linux-64::freetype-2.10.4-h0708190_1
get_version conda-forge/noarch::get_version-2.1-py_1
h5py conda-forge/linux-64::h5py-2.10.0-nompi_py37hf7afa78_105
hdf5 conda-forge/linux-64::hdf5-1.10.6-nompi_h6a2412b_1114
idna conda-forge/noarch::idna-2.10-pyh9f0ad1d_0
imagesize conda-forge/noarch::imagesize-1.2.0-py_0
importlib-metadata conda-forge/noarch::importlib-metadata-1.7.0-pyhd8ed1ab_1
importlib_metadata conda-forge/noarch::importlib_metadata-1.7.0-hd8ed1ab_1
jinja2 conda-forge/noarch::jinja2-2.11.2-pyh9f0ad1d_0
joblib conda-forge/noarch::joblib-0.16.0-py_0
jpeg conda-forge/linux-64::jpeg-9d-h36c2ea0_0
kiwisolver conda-forge/linux-64::kiwisolver-1.2.0-py37h99015e2_1
krb5 conda-forge/linux-64::krb5-1.17.2-h926e7f8_0
lcms2 conda-forge/linux-64::lcms2-2.12-hddcbb42_0
legacy-api-wrap conda-forge/noarch::legacy-api-wrap-1.2-py_0
libblas conda-forge/linux-64::libblas-3.9.0-8_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-8_openblas
libcurl conda-forge/linux-64::libcurl-7.71.1-hcdd3856_3
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libgfortran-ng conda-forge/linux-64::libgfortran-ng-9.3.0-hff62375_18
libgfortran5 conda-forge/linux-64::libgfortran5-9.3.0-hff62375_18
liblapack conda-forge/linux-64::liblapack-3.9.0-8_openblas
libllvm10 conda-forge/linux-64::libllvm10-10.0.1-he513fc3_3
libopenblas conda-forge/linux-64::libopenblas-0.3.12-pthreads_h4812303_1
libpng conda-forge/linux-64::libpng-1.6.37-h21135ba_2
libssh2 conda-forge/linux-64::libssh2-1.9.0-ha56f1ee_6
libtiff conda-forge/linux-64::libtiff-4.2.0-hdc55705_0
libwebp-base conda-forge/linux-64::libwebp-base-1.2.0-h7f98852_2
llvmlite conda-forge/linux-64::llvmlite-0.34.0-py37h5202443_2
loompy bioconda/noarch::loompy-2.0.16-py_0
lz4-c conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_0
lzo conda-forge/linux-64::lzo-2.10-h516909a_1000
markupsafe conda-forge/linux-64::markupsafe-1.1.1-py37h5e8e339_3
matplotlib conda-forge/linux-64::matplotlib-3.3.1-1
matplotlib-base conda-forge/linux-64::matplotlib-base-3.3.1-py37hd478181_1
mock conda-forge/linux-64::mock-4.0.2-py37hc8dfbb8_1
natsort conda-forge/noarch::natsort-7.0.1-py_0
networkx conda-forge/noarch::networkx-2.5-py_0
numba conda-forge/linux-64::numba-0.51.2-py37h9fdb41a_0
numexpr conda-forge/linux-64::numexpr-2.7.1-py37h9fdb41a_3
numpy conda-forge/linux-64::numpy-1.19.1-py37h7ea13bd_2
olefile conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1
packaging conda-forge/noarch::packaging-20.4-pyh9f0ad1d_0
pandas conda-forge/linux-64::pandas-1.1.2-py37h3340039_0
patsy conda-forge/noarch::patsy-0.5.1-py_0
pillow conda-forge/linux-64::pillow-7.2.0-py37h718be6c_2
pycparser conda-forge/noarch::pycparser-2.20-pyh9f0ad1d_2
pygments conda-forge/noarch::pygments-2.7.0-py_0
pyopenssl conda-forge/noarch::pyopenssl-19.1.0-py_1
pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
pysocks conda-forge/linux-64::pysocks-1.7.1-py37h89c1867_3
pytables conda-forge/linux-64::pytables-3.6.1-py37h0c4f3e0_3
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
pytz conda-forge/noarch::pytz-2020.1-pyh9f0ad1d_0
requests conda-forge/noarch::requests-2.24.0-pyh9f0ad1d_0
scanpy bioconda/noarch::scanpy-1.6.0-py_1
scikit-learn conda-forge/linux-64::scikit-learn-0.23.2-py37hddcf8d6_3
scipy conda-forge/linux-64::scipy-1.5.2-py37h14a347d_2
scvelo bioconda/noarch::scvelo-0.2.2-py_1
seaborn conda-forge/linux-64::seaborn-0.11.0-ha770c72_1
seaborn-base conda-forge/noarch::seaborn-base-0.11.0-pyhd8ed1ab_1
setuptools-scm conda-forge/noarch::setuptools-scm-4.1.2-pyh9f0ad1d_0
setuptools_scm conda-forge/noarch::setuptools_scm-4.1.2-0
sinfo conda-forge/noarch::sinfo-0.3.1-py_0
six conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
snowballstemmer conda-forge/noarch::snowballstemmer-2.0.0-py_0
sphinx conda-forge/noarch::sphinx-3.2.1-py_0
sphinxcontrib-app~ conda-forge/noarch::sphinxcontrib-applehelp-1.0.2-py_0
sphinxcontrib-dev~ conda-forge/noarch::sphinxcontrib-devhelp-1.0.2-py_0
sphinxcontrib-htm~ conda-forge/noarch::sphinxcontrib-htmlhelp-1.0.3-py_0
sphinxcontrib-jsm~ conda-forge/noarch::sphinxcontrib-jsmath-1.0.1-py_0
sphinxcontrib-qth~ conda-forge/noarch::sphinxcontrib-qthelp-1.0.3-py_0
sphinxcontrib-ser~ conda-forge/noarch::sphinxcontrib-serializinghtml-1.1.4-py_0
statsmodels conda-forge/linux-64::statsmodels-0.12.0-py37h161383b_1
stdlib-list conda-forge/linux-64::stdlib-list-0.6.0-py37_0
tbb conda-forge/linux-64::tbb-2020.2-h4bd325d_4
threadpoolctl conda-forge/noarch::threadpoolctl-2.1.0-pyh5ca1d4c_0
toml conda-forge/noarch::toml-0.10.1-pyh9f0ad1d_0
tornado conda-forge/linux-64::tornado-6.0.4-py37h8f50634_2
tqdm conda-forge/noarch::tqdm-4.49.0-pyh9f0ad1d_0
typing conda-forge/noarch::typing-3.7.4.3-pyhd8ed1ab_2
umap-learn conda-forge/linux-64::umap-learn-0.4.6-py37hc8dfbb8_0
urllib3 conda-forge/noarch::urllib3-1.25.10-py_0
zipp conda-forge/noarch::zipp-3.1.0-py_0
zstd conda-forge/linux-64::zstd-1.4.9-ha95c52a_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2021.1.19-~ --> conda-forge::ca-certificates-2020.12.5-ha878542_0
certifi pkgs/main::certifi-2020.12.5-py37h06a~ --> conda-forge::certifi-2020.6.20-py37he5f6b98_2
openssl pkgs/main::openssl-1.1.1k-h27cfd23_0 --> conda-forge::openssl-1.1.1k-h7f98852_0
The following packages will be DOWNGRADED:
pip 21.0.1-pyhd8ed1ab_0 --> 20.2.3-py_0
wheel 0.36.2-pyhd3deb0d_0 --> 0.35.1-pyh9f0ad1d_0
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Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.9.2
Please update conda by running
$ conda update -n base -c defaults condacomputing neighbors
finished (0:00:17) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:02) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
computing velocities
finished (0:00:01) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph
... 100%
finished (0:00:02) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
computing terminal states
identified 2 regions of root cells and 3 regions of end points .
finished (0:00:00) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
--> added 'velocity_length' (adata.obs)
--> added 'velocity_confidence' (adata.obs)
--> added 'velocity_confidence_transition' (adata.obs)sce.sperm$pseudotime <- velo.out$velocity_pseudotimeembedded <- embedVelocity( reducedDim(sce.sperm, "TSNE"), velo.out )Note: using the 'X' assay as the X matrixcomputing velocity embedding
finished (0:00:04) --> added
'velocity_target', embedded velocity vectors (adata.obsm)grid.df <- gridVectors( reducedDim(sce.sperm, "TSNE"), embedded, resolution=30 )plotTSNE( sce.sperm, colour_by="pseudotime", point_alpha=0.3 ) +
geom_segment(
data=grid.df,
mapping=aes( x=start.1, y=start.2, xend=end.1, yend=end.2 ),
arrow=arrow( length=unit(0.05, "inches"), type="closed" )
)
Document software
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8
Matrix products: default
BLAS: /home/idies/R/lib64/R/lib/libRblas.so
LAPACK: /home/idies/R/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils
[7] datasets methods base
other attached packages:
[1] velociraptor_1.0.0 scater_1.18.6
[3] ggplot2_3.3.3 scran_1.18.5
[5] scuttle_1.0.4 ensembldb_2.14.0
[7] AnnotationFilter_1.14.0 GenomicFeatures_1.42.2
[9] AnnotationDbi_1.52.0 scRNAseq_2.4.0
[11] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0
[13] Biobase_2.50.0 GenomicRanges_1.42.0
[15] GenomeInfoDb_1.26.4 IRanges_2.24.1
[17] S4Vectors_0.28.1 BiocGenerics_0.36.0
[19] MatrixGenerics_1.2.1 matrixStats_0.58.0
loaded via a namespace (and not attached):
[1] Rtsne_0.15
[2] ggbeeswarm_0.6.0
[3] colorspace_2.0-0
[4] ellipsis_0.3.1
[5] bluster_1.0.0
[6] XVector_0.30.0
[7] BiocNeighbors_1.8.2
[8] rstudioapi_0.13
[9] farver_2.1.0
[10] bit64_4.0.5
[11] interactiveDisplayBase_1.28.0
[12] fansi_0.4.2
[13] xml2_1.3.2
[14] sparseMatrixStats_1.2.1
[15] cachem_1.0.4
[16] knitr_1.31
[17] jsonlite_1.7.2
[18] Rsamtools_2.6.0
[19] dbplyr_2.1.0
[20] shiny_1.6.0
[21] BiocManager_1.30.10
[22] compiler_4.0.3
[23] httr_1.4.2
[24] basilisk_1.2.1
[25] dqrng_0.2.1
[26] assertthat_0.2.1
[27] Matrix_1.2-18
[28] fastmap_1.1.0
[29] lazyeval_0.2.2
[30] limma_3.46.0
[31] later_1.1.0.1
[32] BiocSingular_1.6.0
[33] htmltools_0.5.1.1
[34] prettyunits_1.1.1
[35] tools_4.0.3
[36] rsvd_1.0.3
[37] igraph_1.2.6
[38] gtable_0.3.0
[39] glue_1.4.2
[40] GenomeInfoDbData_1.2.4
[41] dplyr_1.0.5
[42] rappdirs_0.3.3
[43] Rcpp_1.0.6
[44] vctrs_0.3.6
[45] Biostrings_2.58.0
[46] zellkonverter_1.0.3
[47] ExperimentHub_1.16.0
[48] rtracklayer_1.50.0
[49] DelayedMatrixStats_1.12.3
[50] xfun_0.22
[51] stringr_1.4.0
[52] beachmat_2.6.4
[53] mime_0.10
[54] lifecycle_1.0.0
[55] irlba_2.3.3
[56] statmod_1.4.35
[57] XML_3.99-0.5
[58] AnnotationHub_2.22.0
[59] edgeR_3.32.1
[60] basilisk.utils_1.2.2
[61] zlibbioc_1.36.0
[62] scales_1.1.1
[63] hms_1.0.0
[64] promises_1.2.0.1
[65] ProtGenerics_1.22.0
[66] yaml_2.2.1
[67] curl_4.2
[68] reticulate_1.18
[69] gridExtra_2.3
[70] memoise_2.0.0
[71] biomaRt_2.46.3
[72] stringi_1.5.3
[73] RSQLite_2.2.3
[74] BiocVersion_3.12.0
[75] filelock_1.0.2
[76] BiocParallel_1.24.1
[77] rlang_0.4.10
[78] pkgconfig_2.0.3
[79] bitops_1.0-6
[80] evaluate_0.14
[81] lattice_0.20-41
[82] purrr_0.3.4
[83] labeling_0.4.2
[84] GenomicAlignments_1.26.0
[85] bit_4.0.4
[86] tidyselect_1.1.0
[87] magrittr_2.0.1
[88] R6_2.5.0
[89] generics_0.1.0
[90] DelayedArray_0.16.2
[91] DBI_1.1.1
[92] pillar_1.5.1
[93] withr_2.4.1
[94] RCurl_1.98-1.2
[95] tibble_3.1.0
[96] crayon_1.4.1
[97] utf8_1.1.4
[98] BiocFileCache_1.14.0
[99] rmarkdown_2.7
[100] viridis_0.5.1
[101] progress_1.2.2
[102] locfit_1.5-9.4
[103] grid_4.0.3
[104] blob_1.2.1
[105] digest_0.6.27
[106] xtable_1.8-4
[107] httpuv_1.5.5
[108] openssl_1.4.3
[109] munsell_0.5.0
[110] viridisLite_0.3.0
[111] beeswarm_0.3.1
[112] vipor_0.4.5
[113] askpass_1.1 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