JetBrains-Research washu issues

JetBrains-Research / washu

Reproducible and scalable technical pipelines for ChIP-Seq and RNA-Seq processing

https://artyomovlab.wustl.edu/aging

MIT License

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ValueError: cannot resize this array: it does not own its data

#78 beetlejuice007 closed 4 years ago
3
Consider using snakemake for pipeline description

#77 olegs closed 5 years ago
1
Effective genome size calculations seems to be incorrect.

#76 iromeo opened 5 years ago
1
ChIP-seq pipeline and double file filtering

#75 dievsky opened 6 years ago
10
Extract tags bigwigs creation from `signals.sh` script

#74 olegs opened 6 years ago
0
ULI-ChIP-seq pipeline

#73 dievsky opened 6 years ago
1
ChipSeq pipeline: Zero GAP for SICER is used for H3K36me3 GSE112622

#72 iromeo closed 6 years ago
1
MACS2 doesn't detect SE/PE automatically (at least for our bam files)

#71 iromeo opened 6 years ago
5
Cleanup: remove multiple WORKDIRs processing from parallel scripts

#70 olegs opened 6 years ago
0
Unable to pull biolabs/uli-pipeline docker image

#69 olegs closed 6 years ago
3
pipeline_chipseq.py and reproducibility

#68 dievsky opened 6 years ago
15
BedMetrics: support dataset *.yaml as failed tracks

#67 iromeo opened 6 years ago
0
Signal processing fails to calculate frip

#66 iromeo closed 6 years ago
1
Cannot run signals.sh: mkdir: cannot create directory

#65 iromeo closed 6 years ago
1
mm10 is not recognised by SICER step

#64 olegs closed 6 years ago
2
Wget index files

#63 PetrTsurinov closed 6 years ago
0
Use peak_calling_summary format to build all the reports.

#62 PetrTsurinov closed 6 years ago
1
Convert BAM to BED.GZ

#61 olegs closed 6 years ago
1
Create script for constructing IGV and UCSC sessions for aging and encode data

#60 PetrTsurinov closed 6 years ago
1
ChIP-seq difference based on peak number

#59 atsky closed 6 years ago
10
rip.sh only supports BAMs

#58 dievsky closed 6 years ago
4
Signals.sh creates empty fripm result file and doesn't create visualisations

#57 PetrTsurinov closed 6 years ago
1
RSpp package fails to load function from caTools

#56 olegs opened 6 years ago
0
Histone marks width change

#55 iromeo closed 6 years ago
1
GEO downloader doesn't work due to NCBI API changes

#54 iromeo opened 6 years ago
0
Added script for generating cross tool correlation report.

#53 PetrTsurinov closed 6 years ago
0
DiffBind and raw signals processing differs

#52 olegs closed 6 years ago
1
Cross-tool peaks report

#51 PetrTsurinov closed 6 years ago
1
expand_path doesn't resolve symlinks

#50 olegs closed 6 years ago
5
Heatmaps/consistency for different tools of diff analysis

#49 iromeo closed 6 years ago
1
BED.GZ -> BAM not sorted

#48 olegs closed 6 years ago
0
Add _author_ and description to report scripts

#47 olegs closed 6 years ago
1
washu local runs tmp folder are not cleared

#46 olegs closed 6 years ago
2
signals_visualize.py: No module named 'downstream'

#45 iromeo closed 6 years ago
3
Fix project_root_dir

#44 olegs closed 6 years ago
1
#34 consensus

#43 PetrTsurinov closed 6 years ago
0
Annotations evaluation.

#42 iromeo closed 6 years ago
9
Fix FRiP calculation according to ENCODE def

#41 iromeo closed 6 years ago
2
Project structure reorganization

#40 olegs closed 6 years ago
1
Added R^2 chromosome peaks reports script.

#39 PetrTsurinov closed 6 years ago
0
Aggregated errors and cumulative plots

#38 PetrTsurinov closed 6 years ago
1
Combined report, stream consensus, venn/bar plots update

#37 PetrTsurinov closed 6 years ago
0
Consensus abs difference score

#36 iromeo closed 6 years ago
10
Annotate Reactome using offline database files

#35 iromeo opened 6 years ago
5
Allow benchmark_consensus.sh use outliers.csv information

#34 iromeo closed 6 years ago
2
Errors plots made from tuning results

#33 PetrTsurinov closed 6 years ago
0
union.sh add correct error on empty args

#32 olegs closed 6 years ago
0
added script for frip/peaks table construction

#31 PetrTsurinov closed 6 years ago
0
sicer.sh picks up wrong bed file for RIP processing

#30 olegs closed 7 years ago
0
consensus.sh generates confusing names for benchmark result peaks

#29 iromeo closed 7 years ago
1