- #134 Corrected some versions
- #132 Bump version to 2.0.1
- #131 Added design_batcheffect.txt
- #130 Added test_batcheffect to github tests
- #131 Changed Sample_preparations.tsv by adding batch column
- #130 Fixed batch effect bug
- #128 Bump versions to 2.0
- #125 Added test_relevel to github tests, added explanation to usage.md that --species is not necessary if skipping pathway analysis
- #123 Export report volcano plots as SVG; save all plots additionally as PDF
- #122 Add searchable/sortable tables to report
- #118 Add parameter "--input_type" (and change --rawcounts to --gene_counts) to process featurecounts, rsem and salmon output from the new rnaseq; add igenomes.config to process different species
- #104 Add parameter "--skip_pathway_analysis"
- Bump versions to 1.4.0dev
- Add parameter "--min_DE_genes"
- #97 Update pipeline to DSL2
- #107 Add parameter "--skip_rlog"
- #111 Added enhanced volcano plots
- #93 Add parameter "--nsubgenes"
- #115 Template update
- #117 Turned LabID optional for report output in RNAseq_report.Rmd
- Removed assets/report_options.yml
- #110 Changed report to use rlog normalization by default, vst is used if --skip_rlog is enabled
- #127 Allgenes files are not introduced in the PA report section anymore except for volcano plots
- #126 Allgenes files are not published in results anymore. Intermediate results are not zipped and published anymore
- #125 Fixed relevel bug
- #118 Removed blacklist parameter and config and instead added trycatch to ignore pathways with errors
- #105 Fixed relevel and added test_relevel.config
- #106 Fixed
--logFCthresholdbug - #108 Fixed blacklist file not working
- #88 Fixed volcano plot axis
- Bump versions to 1.3.2
- write deseq2 table to file
- Contrast names in report plots
- Convert species name to lower case also in report
- LogFC is also reported in the report and set in volcano plots
- Bump versions to 1.3.1
- Fix bug plots requested boxplots
- Bump versions to 1.3.0dev
- #74 Add option to provide KEGG pathway blacklist
- #74 Make quote param optional
- #74 Make report options optional (default in assets)
- #74 DE gene and pathway summary table
- #75 Boxplot of normalized counts can also be done from non-DE genes.
- #75 More comprehensive variable names and comments
- #74 Pathway analysis only perfomed if at least 2 DE genes
- Added report_options.yml in assets/.
- Skipping pathway analysis for contrasts with no found DE genes.
- Fixed report pvalue typo.
- Major changes in handling contrasts.
- Major improvements to report.
Initial pre-release of qbic-pipelines/rnadeseq, created with the nf-core template.