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databio
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pepatac
A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
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Skipping 1 packages not available: pepr
#250
TianJie327
closed
1 month ago
1
Not remove duplicates
#249
gbloeb
opened
1 year ago
0
looper bug. I change looper version from 1.4.3 to 1.3.0. How can I debug? Please help, thanks!!!!
#248
Conskier
closed
1 month ago
2
update looper reqs for point release v0.10.5
#247
donaldcampbelljr
closed
1 year ago
0
PEPATAC with looper failed with the latest looper and eido
#246
xuebingjie1990
opened
1 year ago
5
Traceback error when running looper for tutorial data
#245
beginnertobioinformatics
closed
1 year ago
4
eido 0.2.0 has changes that break pepatac
#244
molecules
closed
1 year ago
1
There’s NO JAVA in docker image
#243
victorwang123
opened
1 year ago
0
About Run PEPATAC in a container
#242
victorwang123
opened
1 year ago
0
conda install: pip failed, No matching distribution found for codecov==2.1.12
#241
ShannonTown
closed
1 year ago
3
Problem with refgenie
#240
peculiar97
closed
1 year ago
2
Error installing PEPATAC in conda environment || PackageNotFound
#239
unikill066
opened
1 year ago
1
lock file Problem
#238
AnthonyPhosphate
opened
1 year ago
1
tutorial to run from singularity is failing with this error:The following required tool(s) are not callable: macs2
#237
bioarpit1
opened
1 year ago
2
Problem in creating consensus ATAC peaks
#236
gauriprasad08
opened
1 year ago
3
TSSE score appropriate cutoff
#235
ksmtnals90
opened
1 year ago
0
Fastq filter_paired_fq.pl function did not complete successfully
#234
ksmtnals90
opened
1 year ago
0
columns in ref_peaks_coverage.bed
#233
cristanchoa
opened
2 years ago
1
Error at "TSS distance distribution" step
#232
marta-nazzari
opened
2 years ago
0
Issue submitting samples with alternate genomes
#231
rylanci
opened
2 years ago
5
hg38 not exported object from namespace:GenomicDistributionsData
#230
kloot
opened
2 years ago
2
R.utils not in requirements
#229
nsheff
opened
2 years ago
2
argparser is not in requirements
#228
nsheff
opened
2 years ago
1
docker image is missing R packages
#227
nsheff
opened
2 years ago
0
checkinstall bugs
#226
nsheff
opened
2 years ago
1
Where are Supplemental Files 1..4 ?
#225
kloot
closed
2 years ago
1
Installation conflict with fseq
#224
AnthonyPhosphate
opened
2 years ago
3
Error on single end data
#223
lmckinno
opened
2 years ago
1
Cannot run pepatac through docker, conda, or singularity
#222
prm123342
opened
2 years ago
0
Test run fails with this error: skewer (0.2.2): Can not read adapter sequences from FASTA file "tools/NexteraPE-PE.fa"
#221
ybukhman
closed
2 years ago
2
Is there any way to specify the alignment output should be in cram format?
#220
vulpescu
opened
2 years ago
0
Unable to generate count table with reference peaks
#219
gbloeb
opened
2 years ago
4
Unable to generate counts table for consensus peaks (pipeline ignores _ref_peaks_coverage.bed files)
#218
kathleenabadie
opened
2 years ago
0
Is there a way to run IDR with pepatac?
#217
imk1
opened
2 years ago
0
TypeError
#216
namzoo99
opened
2 years ago
11
Documenting way to run pipeline to generate reads in reference peak set
#215
gbloeb
opened
2 years ago
0
Specifying genome size in config.yaml
#214
gbloeb
closed
2 years ago
3
PEPATACr no longer available
#213
gbloeb
closed
2 years ago
2
Singularity Issue
#212
e-arslan
opened
2 years ago
0
update hitaggregator function
#211
ccrobertson
opened
2 years ago
1
Problems with checkinstall for conda installation and pipeline failure
#210
ndrdenny
opened
2 years ago
3
PEPATACr::createStatsSummary Error
#209
hadgie
opened
2 years ago
8
Looper CLI-specified compute settings ignored while running
#208
boothbyi
opened
3 years ago
2
Difficulty integrating with refgenie or manually downloaded assets
#207
gbloeb
opened
3 years ago
2
Conda install issues
#206
gbloeb
closed
3 years ago
2
Problem with parsing of chromosome names that contain | symbol
#205
khorms
closed
3 years ago
1
TSS_hg38 not available in GenomicDistributions package and GenomicDistributionsData package is not installed
#204
hiroyukikato911
closed
3 years ago
1
Question about rCRSd and human_repeats
#203
hiroyukikato911
opened
3 years ago
1
NFR_frac = round(float(nfr) / float(dar), 4) ZeroDivisionError: float division by zero
#202
hiroyukikato911
closed
3 years ago
1
quantitative ATACseq
#201
wangjiawen2013
closed
3 years ago
1
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