bcbio/bcbioR

Issues

• sc normalization and clustering

  #48 opened 3 months ago by lpantano
  0

• sc DE discussion

  #47 opened 3 months ago by lpantano
  0

• Updated common repository of gene sets (hallmark, reactome, etc).

  #19 opened 6 months ago by lpantano
  0

• Support multiple contrasts in the same report

  #36 opened 5 months ago by lpantano
  0

• cutandrun report elements

  #43 opened 3 months ago by abartlett004
  3

• DEseq report discussion

  #45 opened 3 months ago by lpantano
  0

• avoid samples with `-` or other character is not `_alphanumeric`

  #40 opened 3 months ago by lpantano
  1

• DEG rdata annotation assumes human reference

  #41 opened 4 months ago by epartan
  1

• Support comparing multiple DESeq2 results

  #37 opened 5 months ago by lpantano
  0

• add checks for low count genes?

  #35 opened 5 months ago by eberdan
  0

• QC metrics labels to default size be larger

  #5 opened 5 months ago by lpantano
  0

• Options for batch effect in data

  #10 opened 5 months ago by lpantano
  0

• Viridis for Heatmap

  #6 opened 5 months ago by lpantano
  0

• heatmap with genes and samples

  #2 opened 5 months ago by lpantano
  0

• PCA

  #4 opened 5 months ago by lpantano
  0

• Adapt DE report to nf-core

  #15 opened 5 months ago by lpantano
  0

• metrics excluded from nfcore

  #16 opened 5 months ago by abartlett004
  0

• potentially use this package for more palette options

  #34 opened 5 months ago by lpantano
  0

• Feedback in development branch

  #28 opened 5 months ago by lpantano
  1

• make sanitize_datatable into package function

  #29 opened 5 months ago by abartlett004
  0

• check samplesheet function to ensure files exist

  #27 opened 5 months ago by abartlett004
  0

• introduce changes from Emma

  #20 opened 6 months ago by lpantano
  0

• Common repository for lists of protein coding genes

  #18 opened 6 months ago by lpantano
  0

• Common repository (dropbox?) for annotations to add to DE lists

  #17 opened 6 months ago by lpantano
  0

• RUVSeq to be optional

  #9 opened 6 months ago by lpantano
  0

• gene plot with dots

  #1 opened 6 months ago by lpantano
  0

• Interactive volcano plot with glXYPlot

  #12 opened 7 months ago by upendrabhattarai
  0

• similar projects

  #13 opened 7 months ago by lpantano
  0

• Enrichment analysis flexibility

  #11 opened 7 months ago by lpantano
  0

• DE - coefficient vs contrasts

  #8 opened 7 months ago by lpantano
  0

• DE_template_example.Rmd - subset discussion

  #7 opened 7 months ago by lpantano
  0

• get sc script from Noor

  #3 opened 7 months ago by lpantano
  0