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sanjaynagi
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rna-seq-pop
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
https://sanjaynagi.github.io/rna-seq-pop/
MIT License
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variantanalysis in config should override other options
#105
sanjaynagi
opened
1 month ago
0
Improve gsea nb
#104
sanjaynagi
closed
1 month ago
0
freebayes add parameter: min-alternate-fraction 0.05
#103
sanjaynagi
closed
1 month ago
0
add support for clara parabricks
#102
sanjaynagi
closed
2 months ago
0
tidy Snakefile and rule files
#101
sanjaynagi
closed
2 months ago
0
add local db support for snpeff, update config names and restructure .smk rule files
#100
sanjaynagi
closed
2 months ago
1
coverage was not saving logs to file
#99
sanjaynagi
closed
2 months ago
0
allow local snpeff db
#98
sanjaynagi
closed
2 months ago
0
qc_notebook requires fastp output
#97
sanjaynagi
closed
2 months ago
0
error in rule DifferentialIsoformExpression when running test dataset - possible sleuth/R problem?
#96
azurillandfriend
opened
3 months ago
1
small fixes to pca + gwss notebooks
#95
sanjaynagi
closed
4 months ago
0
remove venn diagrams
#94
sanjaynagi
closed
8 months ago
1
matplotlib can't import docstring causes error in checkinputs
#93
azurillandfriend
closed
7 months ago
3
Do not require VCFs if doing GSEA and remove VENN
#92
sanjaynagi
closed
8 months ago
0
provide singularity containers for the conda envs
#91
sanjaynagi
opened
9 months ago
0
Update pythonGenomics env - specific versions of packages
#90
sanjaynagi
closed
11 months ago
0
Make both Gene and isoform DE optional + fix for .xlsx, .csv metadata
#89
sanjaynagi
closed
12 months ago
0
make isoform level DE optional
#88
sanjaynagi
closed
12 months ago
0
Change some config naming to make more sense
#87
sanjaynagi
closed
2 months ago
1
xlsx and csv fail due to common.smk
#86
sanjaynagi
closed
12 months ago
0
fix single-end reads with column input
#85
sanjaynagi
closed
12 months ago
1
Allow xlsx or csv or tsv metadata input
#84
sanjaynagi
closed
1 year ago
0
Allow .tsv or .xlsx or .csv metadata input
#83
sanjaynagi
closed
1 year ago
1
Move old scripts to scripts/old/
#82
sanjaynagi
closed
1 year ago
0
Configure conda envs so they work with conda channel priority = strict
#81
sanjaynagi
opened
1 year ago
0
Implement rna-seq-pop results book
#80
sanjaynagi
closed
1 year ago
2
remove cutadapt and add fastp
#79
sanjaynagi
closed
1 year ago
1
Ensure meets FAIR principles and add to workflowhub.eu
#78
sanjaynagi
opened
1 year ago
0
Create Jupyter book and convert appropriate analyses to ipynb and papermill rather than py
#77
sanjaynagi
closed
1 year ago
2
go on a code removal and tidying spree
#76
sanjaynagi
closed
1 year ago
1
docs, config update, name changes, tidying, no window choices
#75
sanjaynagi
closed
1 year ago
2
gsea fdr
#74
sanjaynagi
closed
1 year ago
0
move gwss into different folders based on window size
#73
sanjaynagi
closed
1 year ago
1
new gsea implementation, hypergeo in python
#72
sanjaynagi
closed
1 year ago
1
Remove large blobs
#71
sanjaynagi
closed
1 year ago
1
remove diffsnps, allow gzipped reference files
#70
sanjaynagi
closed
1 year ago
1
implement own gsea from GAF file
#69
sanjaynagi
closed
1 year ago
0
rule that unzips a .fa.gz ref file
#68
sanjaynagi
closed
1 year ago
1
mv plots to quant
#67
sanjaynagi
closed
1 year ago
1
gzip pfam go
#66
sanjaynagi
closed
1 year ago
0
remove compkaryo and mpileup2readcounts submodules
#65
sanjaynagi
closed
1 year ago
1
remove qualimap, add qc options to config
#64
sanjaynagi
closed
1 year ago
0
fastq table fixes
#63
sanjaynagi
closed
1 year ago
0
In docs, do example analysis of bouake
#62
sanjaynagi
closed
1 year ago
0
fix allele balance use of 'contig' instead of 'chrom', other small fixes
#61
sanjaynagi
closed
1 year ago
0
add tests for main functions in rnaseqpoptools
#60
sanjaynagi
opened
1 year ago
0
check codecov
#59
sanjaynagi
closed
1 year ago
0
add venn and heatmap to documentation
#58
sanjaynagi
closed
1 year ago
1
allow single end reads
#57
sanjaynagi
closed
1 year ago
0
implement single-end read functionality
#56
sanjaynagi
closed
1 year ago
1
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