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sidbdri
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cookiecutter-de_analysis_skeleton
Skeleton for new differential expression analysis project.
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Strand check not taking place?
#226
lweasel
closed
1 month ago
4
Check for choroid plexus contamination
#225
lweasel
closed
2 months ago
2
Remove "NA" section from plot_expression_heatmap() plots
#224
lweasel
closed
2 months ago
1
Installation of transcript_utils and Sargasso fails in initial setup script.
#223
lweasel
closed
3 months ago
1
Fix heatmap
#222
deepalivasoya
closed
2 months ago
2
Check for illegal characters in comparison names
#221
lweasel
closed
2 months ago
3
Mitochondrial graphs overestimate mitochondrial gene percentage
#220
lweasel
closed
11 months ago
0
Moving plots for improved understandibility
#219
lweasel
closed
2 months ago
2
plot_expression_heatmap() broken by duplicate gene names
#218
lweasel
closed
1 year ago
6
Problem plotting gene expression heatmaps
#217
lweasel
closed
1 year ago
4
New D. E. heatmap doesn't select top x up-regulated genes
#216
lweasel
closed
1 year ago
0
issue with rmats dependency in system python3.8
#215
hxin
closed
1 year ago
0
refactor retrieve_fastqs logic
#214
hxin
closed
1 year ago
2
Plot mitochondrial percentages in SAMPLE_DATA order
#213
lweasel
closed
1 year ago
0
Update DESeq2 pre-filtering
#212
lweasel
closed
1 year ago
0
incorrect passing fastq files due to READ1/2_IDENTIFIER setting in paired-end/single-end data
#211
hxin
closed
1 year ago
0
Add PCA plot coloured by mitochondrial gene percentages
#210
lweasel
closed
1 year ago
1
Automatically prepare deliverable results
#209
lweasel
closed
1 year ago
1
Deliver SAMPLE_DATA as CSV/Excel file in distributed results
#208
lweasel
closed
1 year ago
0
Bump certifi from 2020.12.5 to 2022.12.7 in /{{cookiecutter.project_name}}
#207
dependabot[bot]
opened
1 year ago
0
Bump pillow from 9.0.1 to 9.3.0 in /{{cookiecutter.project_name}}
#206
dependabot[bot]
opened
1 year ago
0
Minor mistake in naming of Reactome results
#205
lweasel
closed
2 years ago
1
Slight inconsistency in naming of tx-level results files
#204
lweasel
closed
2 years ago
1
Upgrade to R-4.2.0 / Bioconductor 3.15
#203
lweasel
closed
1 year ago
2
Add check for empty genes.tsv
#202
lweasel
closed
2 years ago
1
Automate writing paper Methods section
#201
lweasel
closed
2 years ago
1
run_jobs_with_shared_memory() currently broken
#200
lweasel
closed
2 years ago
0
Add check for illegal characters in COMPARISON_TABLE
#199
lweasel
closed
2 years ago
1
Add "all features" PCA plots for each comparison
#198
lweasel
closed
2 years ago
0
parallel process can take up too much memory
#197
hxin
closed
2 years ago
4
Add per-comparison volcano plots
#196
lweasel
closed
2 years ago
0
plot_scatter_fpkm() doesn't respect comparison sample filter
#195
lweasel
closed
2 years ago
0
Set betaPrior=FALSE for interaction comparisons in deseq.R
#194
lweasel
closed
2 years ago
0
Merge master -> dev
#193
lweasel
closed
2 years ago
0
Merge dev to master
#192
lweasel
closed
2 years ago
0
Odds ratio calculation fails for reactome when there are no significant pathways
#191
lweasel
closed
2 years ago
2
check_formulas() doesn't work for interaction comparisons?
#190
lweasel
closed
2 years ago
2
Bump numpy from 1.21.0 to 1.22.0 in /{{cookiecutter.project_name}}
#189
dependabot[bot]
closed
2 years ago
0
rMATS4.1.0 script
#188
hxin
closed
2 years ago
0
Add odds ratio for topGO and Reactome results
#187
lweasel
closed
2 years ago
0
Plot top transcripts for TX analysis
#186
lweasel
closed
2 years ago
0
cookiecutter pipeline integration test
#185
hxin
closed
2 years ago
2
R scripts should respect "number_total_threads"
#184
lweasel
closed
2 years ago
0
Bump pillow from 9.0.0 to 9.0.1 in /{{cookiecutter.project_name}}
#183
dependabot[bot]
closed
2 years ago
0
Get transcript level D.E. analysis running again
#182
lweasel
closed
2 years ago
0
Get rMATS analysis running in cookiecutter again
#181
lweasel
closed
2 years ago
1
Parallelise production of gene sets heatmaps
#180
lweasel
closed
2 years ago
0
Bump numpy from 1.20.1 to 1.21.0 in /{{cookiecutter.project_name}}
#179
dependabot[bot]
closed
2 years ago
0
Bump pillow from 8.3.2 to 9.0.0 in /{{cookiecutter.project_name}}
#178
dependabot[bot]
closed
2 years ago
0
Sargasso project is not using enough cores
#177
hxin
closed
2 years ago
1
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