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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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Gene list heatmaps script
#53
sanjaynagi
closed
1 year ago
0
Implement heatmap script
#52
sanjaynagi
closed
1 year ago
0
Make video tutorial/walkthrough
#51
sanjaynagi
closed
1 year ago
2
Implement venn diagrams of expressed genes
#50
sanjaynagi
closed
1 year ago
1
Change syntax for contrasts
#49
sanjaynagi
closed
12 months ago
0
remove use of separate fastq lookup table
#48
sanjaynagi
closed
1 year ago
0
Allow fastq path in metadata - 15.10.22
#47
sanjaynagi
closed
1 year ago
1
Chrom to contig 11 10 22
#46
sanjaynagi
closed
1 year ago
1
Implement Anopheles gambiae AIMs chromosome plot
#45
sanjaynagi
opened
1 year ago
0
simplify summaryStats.py, change method to 20kb windows as used in ms
#44
sanjaynagi
closed
1 year ago
1
Problem installing the rna-seq-pop
#43
dieunelderilus
closed
1 year ago
6
change freebayes min depth param
#42
sanjaynagi
opened
2 years ago
2
add CIs to Variants of interest module
#41
sanjaynagi
closed
2 years ago
1
Change 'chrom' to 'contig'
#40
sanjaynagi
closed
1 year ago
1
allowing custom snpEff databases
#39
vmkalbskopf
closed
1 year ago
4
Adapting workflow to other species
#38
vmkalbskopf
closed
1 year ago
67
Check for signals.tsv
#37
sanjaynagi
closed
3 years ago
1
remove need for DE contrasts rule
#36
sanjaynagi
closed
3 years ago
1
allow fastq files to be specified in units.tsv
#35
sanjaynagi
closed
3 years ago
2
Split regions by coverage
#34
sanjaynagi
closed
3 years ago
0
add more options in config for everything
#33
sanjaynagi
closed
3 years ago
1
split the genome into freebayes jobs of roughly equal size
#32
sanjaynagi
closed
3 years ago
1
progressiveDE - allow multiple groups comparisons
#31
sanjaynagi
closed
3 years ago
1
add some resources directives
#30
sanjaynagi
closed
1 year ago
0
load individual packages instead of whole 'tidyverse'
#29
sanjaynagi
closed
3 years ago
2
check that you can vary ploidy
#28
sanjaynagi
closed
3 years ago
2
name all params and snakemake@ in scripts
#27
sanjaynagi
closed
3 years ago
1
rename scripts
#26
sanjaynagi
closed
3 years ago
1
rename logs
#25
sanjaynagi
closed
3 years ago
1
Documentation
#24
sanjaynagi
closed
1 year ago
1
automatically generate desired outputs files
#23
sanjaynagi
closed
3 years ago
1
selection scan window size
#22
sanjaynagi
closed
3 years ago
1
Improve Volcano plot aesthetics
#21
sanjaynagi
closed
3 years ago
3
fix labels on read counts PCA
#20
sanjaynagi
closed
3 years ago
2
complete gene set enrichment script and integrate
#19
sanjaynagi
closed
3 years ago
1
Fix AIMS legend position
#18
sanjaynagi
closed
3 years ago
2
Windowed Fst scan
#17
sanjaynagi
closed
3 years ago
0
look for introgression signals
#16
sanjaynagi
closed
3 years ago
1
only do FST/PBS for genes of high enough depth
#15
sanjaynagi
closed
1 year ago
1
Report SNP statistics
#14
sanjaynagi
closed
3 years ago
2
Z transform fst values
#13
sanjaynagi
closed
1 year ago
0
get coverage script
#12
sanjaynagi
closed
3 years ago
1
store figs in /plots folders
#11
sanjaynagi
closed
3 years ago
0
add continuous integration with travis
#10
sanjaynagi
closed
3 years ago
2
run statement to check input files
#9
sanjaynagi
closed
3 years ago
0
implement AIMs analysis for Anopheles gambiae datasets
#8
sanjaynagi
closed
3 years ago
1
Decide what to do if multiple species regarding reference genomes
#7
sanjaynagi
closed
3 years ago
3
edit scripts to take snakemake params
#6
sanjaynagi
closed
3 years ago
3
put rules into groups to be executed together
#5
sanjaynagi
closed
3 years ago
0
expand config.yaml
#4
sanjaynagi
closed
3 years ago
2
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