qbic-pipelines/rnadeseq

Issues

• Double-colored bar in enrichment plot, some slashes missing

  #185 opened 8 months ago by WackerO
  1

• Order the pathway heatmaps according to condition

  #224 opened 8 months ago by LaurenceKuhl
  4

• Reduce pathway heatmaps to relevant samples

  #230 opened 8 months ago by WackerO
  0

• Use --relevel parameter for PCA plotting

  #222 opened a year ago by qbicStefanC
  1

• Volcano plots and PCA plot don't have correct x and y axis dimensions

  #183 opened 8 months ago by LaurenceKuhl
  1

• Improve documentation: Troubleshooting

  #156 opened 2 years ago by SusiJo
  4

• Update to final report.zip

  #119 opened 9 months ago by qbicStefanC
  4

• A question about how setting metadata for Nonmodel plant species

  #153 opened 9 months ago by zhangwenda0518
  2

• The destination path is too long error on windows

  #166 opened 9 months ago by WackerO
  1

• star salmon doesn't output round values

  #187 opened 9 months ago by LaurenceKuhl
  2

• Adding support for clusterProfiler

  #135 opened 9 months ago by ggabernet
  1

• Switch multiqc for deseq report

  #137 opened 9 months ago by WackerO
  1

• Save pipeline info to zip

  #223 opened 9 months ago by WackerO
  1

• Genes without 'gene_name' wont be shown in Volcano plot

  #216 opened a year ago by d4straub
  3

• If no enriched pathway is found, it simply states so instead of throwing an error

  #210 opened 2 years ago by jonoave
  1

• Include background gene list for pathway analysis

  #201 opened 2 years ago by ggabernet
  1

• Remove `multiqc` and `software_versions.yml` from rnadeseq report

  #171 opened 2 years ago by ggabernet
  3

• Software versions

  #157 opened 2 years ago by WackerO
  1

• ## Enriched pathways not displayed properly

  #194 opened 2 years ago by WackerO
  1

• Unreadable heatmap ticks

  #186 opened 2 years ago by WackerO
  1

• Add sample labels to PCA plot RNAseq_report.htm

  #143 opened 2 years ago by jonoave
  3

• Legend is cutoff for enriched pathway plots

  #184 opened 2 years ago by WackerO
  1

• Contrast that is not included in design throws error

  #170 opened 2 years ago by WackerO
  0

• Do another lookover of code and docu

  #158 opened 2 years ago by WackerO
  4

• Updating file `pipeline_info/results_description.html`

  #121 opened 2 years ago by qbicStefanC
  3

• Do a template update

  #161 opened 2 years ago by WackerO
  1

• Rename the parameter --skip_pathway_analysis to --run_pathway_analysis and have the default set to 'false'

  #168 opened 2 years ago by qbicStefanC
  1

• MultiQC now has a "-fw" in the sample name leading to duplicate lines

  #114 opened 2 years ago by LaurenceKuhl
  1

• feature - The contrast list is not taken into account for boxplots

  #89 opened 2 years ago by LaurenceKuhl
  0

• Fix volcano and enrichmeht plot layout

  #160 opened 2 years ago by WackerO
  1

• Improve error message salmon input

  #154 opened 2 years ago by SusiJo
  2

• Add pval_threshold analogous to logFC

  #138 opened 2 years ago by WackerO
  1

• add checks if provided contrast_names and factors are in metadata

  #141 opened 2 years ago by WackerO
  1

• Look again at species library

  #142 opened 2 years ago by WackerO
  1

• Docu of how to use batch effect is misleading

  #155 opened 2 years ago by SusiJo
  3

• Rename versions to software_versions

  #144 opened 2 years ago by WackerO
  1

• Check if transcript ID works for all relevant gtf files

  #146 opened 2 years ago by WackerO
  0

• Pathway analysis folder should not be created if pathway analysis was set to FALSE

  #120 opened 2 years ago by qbicStefanC
  2

• Clarify incompatible columns if counttable and metadata differ

  #139 opened 2 years ago by WackerO
  1

• Make sure nsub works

  #140 opened 2 years ago by WackerO
  1

• Separate RNAseq results from rnadeseq results

  #98 opened 2 years ago by ggabernet
  1

• Sample information - order by QBiC barcodes

  #116 opened 2 years ago by LaurenceKuhl
  1

• Make rlog transformation optional

  #99 opened 3 years ago by SusiJo
  2

• Pipeline fails when using `--relevel`

  #94 opened 3 years ago by SusiJo
  0

• Make --species optional if no pathway analysis is done

  #91 opened 3 years ago by d4straub
  1

• Volcano plots have capped logFC on the x axis

  #88 opened 3 years ago by LaurenceKuhl
  1

• Replace species parameter with parameter for library

  #112 opened 3 years ago by WackerO
  1

• Param `--logFCthreshold` is not working properly

  #100 opened 3 years ago by SusiJo
  1

• Make pathway analysis optional

  #102 opened 3 years ago by SusiJo
  3

• Pipeline fails when running with `test` configs

  #95 opened 3 years ago by SusiJo
  1