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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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Number of regions
#200
wangjiawen2013
closed
3 years ago
3
Dev
#199
jpsmith5
closed
3 years ago
0
Feat refgenie plugin
#198
jpsmith5
closed
3 years ago
0
TSS enrichment taking a long time to process
#197
badusername21
closed
3 years ago
1
Should checkinstall check for refgenie assets?
#196
nsheff
closed
3 years ago
3
Issue with "psutil.NoSuchProcess process no longer exists"
#195
lmckinno
closed
3 years ago
1
question about setting number of cores
#194
pegahtak
closed
3 years ago
4
Speeding up pepatac for tiny samples
#193
nsheff
closed
3 years ago
1
Updating readme
#192
nsheff
closed
3 years ago
0
logos are broken
#191
nsheff
closed
3 years ago
0
Making pepatac installable
#190
nsheff
opened
3 years ago
2
checkinstall pipe from web
#189
nsheff
closed
3 years ago
6
Rerun sample after failed
#188
lmckinno
closed
3 years ago
1
Refgenie integration
#187
nsheff
closed
3 years ago
14
Clarify error messages for missing assets
#186
nsheff
closed
3 years ago
2
No address associated with hostname
#185
nsheff
closed
3 years ago
3
fseq2 cannot be specified as a peak caller in PEPATAC v0.9.16
#184
kwcurrin
closed
3 years ago
1
fseq2 missing output folder assignment
#183
kwcurrin
closed
3 years ago
1
specifying cpu and mem requirements
#182
ccrobertson
closed
3 years ago
4
Dev
#181
jpsmith5
closed
3 years ago
0
HMMRATAC as peak caller - Peaks folder output
#180
PratimaNL
closed
3 years ago
3
fwrite error in PEPATAC.R
#179
kwcurrin
closed
3 years ago
2
Sample-specific yaml file is not generated for the first sample if the submission folder doesn't exist
#178
kwcurrin
closed
3 years ago
4
Are fixed peaks defined relative to peak center or summit?
#177
kwcurrin
closed
3 years ago
2
output narrowPeaks
#176
wangjiawen2013
closed
3 years ago
1
assets doesn't exist
#175
wangjiawen2013
opened
3 years ago
13
Generating count table
#174
wangjiawen2013
closed
3 years ago
1
add citation
#173
nsheff
closed
3 years ago
1
is it possible to use aligned bam files as input ?
#172
pegahtak
closed
3 years ago
2
Dev
#171
jpsmith5
closed
3 years ago
0
Sample with multiple R1 and R2 reads
#170
arpanda
closed
3 years ago
3
Dev
#169
jpsmith5
closed
3 years ago
0
help with extended tutorial
#168
pegahtak
closed
3 years ago
7
NCList_find_overlaps_in_groups
#167
Sethupathy-Lab
closed
3 years ago
5
Use https for link
#166
nsheff
closed
3 years ago
1
PEPATAC error: ConnectionResetError: [Errno 104] Connection reset by peer
#165
taherimo
closed
3 years ago
11
set env vars in the "Install and run test example" tutorial
#164
stolarczyk
closed
3 years ago
2
running example project
#163
pegahtak
closed
3 years ago
9
cannot run demo
#162
Honchkrow
closed
3 years ago
1
Feat biocproject
#161
jpsmith5
closed
4 years ago
0
Some questions
#160
trn30
closed
3 years ago
1
pepatac bulker crate issues with /etc/resolv.conf, genrich, and macs2/python problems
#159
rcorces
closed
3 years ago
15
Help using pepatac with a non-reference genome
#158
josruirod
closed
3 years ago
9
MACS2 step failing because the input bed file does not have strand info?
#157
josruirod
closed
4 years ago
11
Help with PEPATAC and non-model reference. "Required assets not existing"
#156
josruirod
closed
4 years ago
4
samtools v1.11 compatibility?
#155
jpsmith5
closed
4 years ago
5
Help with the extended tutorial
#154
josruirod
closed
4 years ago
5
ImportError: cannot import name 'get_logger' from 'peppy.utils'
#153
josruirod
closed
4 years ago
7
Error in single end fastq file
#152
hiroyukikato911
closed
4 years ago
6
Normalization Rscript failed
#151
gbloeb
closed
4 years ago
2
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