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snakemake-workflows
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rna-seq-kallisto-sleuth
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
MIT License
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chore(main): release 2.4.3
#69
github-actions[bot]
closed
1 year ago
1
fix: Update sleuth conda environment and add multithreading to kallisto quant
#68
Austin-s-h
closed
1 year ago
0
fix: Feature/update cutadapt wrapper
#67
Austin-s-h
closed
1 year ago
2
can base_level be multiple if has many groups?
#66
whiteorchid
closed
1 year ago
2
chore(main): release 2.4.2
#65
github-actions[bot]
closed
1 year ago
1
fix: fix gene-level p-value adjustment (use Benjamini-Hochberg instead of Bonferroni-Holm)
#64
johanneskoester
closed
1 year ago
0
fix: for some rules, omit software env when caching
#63
johanneskoester
closed
1 year ago
0
feat: Support for 3-prime RNA sequencing
#62
manuelphilip
closed
1 year ago
0
fix: fix default minimum p-value in fgsea
#61
johanneskoester
closed
1 year ago
0
chore(main): release 2.4.1
#60
github-actions[bot]
closed
1 year ago
1
fix: correct default value for representative_transcripts and check for existence of path
#59
johanneskoester
closed
1 year ago
0
chore(main): release 2.4.0
#58
github-actions[bot]
closed
2 years ago
1
ValidationError: 'nperm' is a required property
#57
cmeesters
closed
2 years ago
3
config.yaml is not part of the release download
#56
cmeesters
closed
2 years ago
1
adjust fgsea.R script to changes in fgsea() function interface
#55
dlaehnemann
closed
2 years ago
0
Fix: fixed custom representative transcript handling; various little bug fixes
#54
johanneskoester
closed
2 years ago
0
InputFunctionException in line 29 .../quant.smk
#53
amitfenn
opened
2 years ago
1
feat: join sample expressions into diffexp table
#52
johanneskoester
closed
2 years ago
0
feat: extended diffexp tables with gene description
#51
johanneskoester
closed
3 years ago
0
chore: Bump r-base and related package versions to R 4.1
#50
tedil
closed
3 years ago
0
handle empty results in goatools
#49
johanneskoester
closed
3 years ago
0
Fixes and workarounds derived from running the pipeline on mouse data
#48
johanneskoester
closed
3 years ago
0
feat: generate batch effect corrected matrix output
#47
johanneskoester
closed
3 years ago
0
Implement canonical transcript support.
#46
johanneskoester
closed
2 years ago
0
Interactive volcano plots
#45
tedil
closed
3 years ago
2
plot-bootstrap.R: fix script to handle an empty genes of interest list in config.yaml
#44
dlaehnemann
closed
3 years ago
0
automatically download reference
#43
dlaehnemann
closed
3 years ago
0
include Zenodo DOI
#42
dlaehnemann
closed
3 years ago
0
Migrate to new workflow usage
#41
dlaehnemann
closed
3 years ago
0
Miscellaneous fixes
#40
tedil
closed
3 years ago
0
Extend p value plot captions
#29
dlaehnemann
closed
3 years ago
0
fgsea.r: unnest leadingEdge and create correct columns for empty data
#28
dlaehnemann
closed
3 years ago
1
Missing input files for rule kallisto_index:
#27
trishorts
closed
1 year ago
2
ensure that biomart getBM() does not use a cache (this has led to failures)
#26
dlaehnemann
closed
4 years ago
0
remove .test/report.html as it is too big (17 Mb is > 10 Mb GitHub limit)
#25
dlaehnemann
closed
4 years ago
0
problem with creating new copy as a template
#24
dence
closed
4 years ago
1
Differential splicing analysis.
#23
johanneskoester
closed
2 years ago
0
Ihw fdr control
#22
AntonieV
closed
4 years ago
2
Bootstrap plots checkpoint to report directory
#21
dlaehnemann
closed
4 years ago
7
Get rid of checkpoints
#20
johanneskoester
opened
4 years ago
0
only remove sample rows with NAs in model-relevant columns
#19
dlaehnemann
closed
4 years ago
0
fgsea.R: fix ext_gene ties equivalent to ens_gene ties in sleuth_diffexp
#18
dlaehnemann
closed
4 years ago
0
pin all uses of select() to a library, avoid AnnotationDbi vs. dplyr collisions
#17
dlaehnemann
closed
4 years ago
0
merge samples in kallisto_quant step
#16
dlaehnemann
opened
4 years ago
2
test if SIGNOR database can be used by SPIA pathway enrichment analysis
#15
dlaehnemann
opened
4 years ago
0
Plots v2
#14
AntonieV
closed
4 years ago
1
any name for diffexp grouping column, fix no custom_transcripts, future-proof column select()
#13
dlaehnemann
closed
4 years ago
0
volcano plot script and respective rules
#12
dlaehnemann
closed
4 years ago
1
Docker run fail when using the "use this template" import
#11
mgalland
closed
4 years ago
2
Changes in `units.tsv` do not promt a rerun of the workflow
#10
HenningTimm
opened
4 years ago
0
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