Softwares:

samtools==1.10
bedtools==2.26.0
macs2==2.1.1.20160309
TOBIAS==0.13.2
Bowtie2==2.3.4.1
HINT==0.13.2
R==4.1.0
Python==3.8.16

Python packages:

tensorflow==2.6.2
Bio==1.5.5
h5py==2.10.0
keras==2.11.0
keras_nightly==2.5.0.dev2021032900
matplotlib==3.5.1
numpy==1.19.5
palantir==1.0.0
pandas==1.5.3
pybedtools==0.8.1
pyranges==0.0.120
pysam==0.18.0
scikit_learn==1.2.1
scipy==1.7.3
seaborn==0.11.2
torch==1.13.1
tqdm==4.62.3

R packages:

assertthat==0.2.1
base64enc==0.1-3
Biobase==2.52.0
BiocGenerics==0.38.0
BiocIO==1.2.0
BiocParallel==1.26.2
Biostrings==2.60.2
bit==4.0.4
bit64==4.0.5
bitops==1.0-7
BuenColors==0.5.6
Cairo==1.5-12.2
caTools==1.18.2
circlize==0.4.13
cladoRcpp==0.15.1
cli==3.2.0
clue==0.3-59
cluster==2.1.2
codetools==0.2-18
collapse==1.5.3
colorspace==2.0-3
compiler==4.1.3
ComplexHeatmap==2.8.0
crayon==1.5.0
data.table==1.14.2
DBI==1.1.2
DelayedArray==0.18.0
digest==0.6.29
doParallel==1.0.16
doSNOW==1.0.19
dplyr==1.0.8
ellipsis==0.3.2
evaluate==0.15
fansi==1.0.2
farver==2.1.0
fastmap==1.1.0
FigR==0.1.0
foreach==1.5.1
generics==0.1.2
GenomeInfoDb==1.28.4
GenomeInfoDbData==1.2.6
GenomicAlignments==1.28.0
GenomicRanges==1.44.0
GetoptLong==1.0.5
ggplot2==3.3.3
GlobalOptions==0.1.2
glue==1.6.2
gtable==0.3.0
gtools==3.9.2
hdf5r==1.3.3
htmltools==0.5.2
IRanges==2.26.0
iterators==1.0.13
jsonlite==1.8.0
keras==2.4.0
knitr==1.37
labeling==0.4.2
lattice==0.20-45
lifecycle==1.0.1
magick==2.7.2
magrittr==2.0.2
MASS==7.3-55
Matrix==1.4-0
MatrixGenerics==1.4.3
matrixStats==0.61.0
munsell==0.5.0
patchwork==1.1.1
pbapply==1.4-3
pbmcapply==1.5.0
pillar==1.7.0
pkgconfig==2.0.3
png==0.1-7
purrr==0.3.4
R6==2.5.1
RColorBrewer==1.1-3
Rcpp==1.0.7
RcppArmadillo==0.11.0.0.0
RcppEigen==0.3.3.9.1
RCurl==1.98-1.3
restfulr==0.0.13
reticulate==1.20
rjson==0.2.21
rlang==1.0.2
rmarkdown==2.13
Rsamtools==2.8.0
rstudioapi==0.13
rtracklayer==1.52.1
S4Vectors==0.30.2
scales==1.2.0
shape==1.4.6
snow==0.4-3
stringi==1.7.6
stringr==1.4.0
SummarizedExperiment==1.22.0
tensorflow==2.5.0
tfruns==1.5.0
tibble==3.1.6
tidyselect==1.1.2
tools==4.1.3
utf8==1.2.2
vctrs==0.3.8
whisker==0.4
withr==2.5.0
xfun==0.30
XML==3.99-0.9
XVector==0.32.0
yaml==2.3.5
zeallot==0.1.0
zlibbioc==1.38.0
