nf-core/scdownstream

Issues

• Create nf-core subworkflow for Cellbender empty droplet detection

  #111 opened 14 days ago by nictru
  1

• scanpy GPU containers fail

  #105 opened 21 days ago by KallyopeComp
  5

• Add option for per-sample specification of doublet detection thresholds

  #88 opened 3 months ago by nictru
  0

• SOLO returns doublet instead of singlets

  #121 opened a month ago by LeonHafner
  0

• Create nf-core module for SOLO

  #115 opened a month ago by nictru
  0

• Create nf-core module for DoubletDetection

  #117 opened a month ago by nictru
  0

• Create nf-core module for scAR

  #114 opened a month ago by nictru
  2

• Create nf-core module for SoupX

  #112 opened a month ago by nictru
  0

• Improve `preprocess_only` implementation

  #108 opened a month ago by nictru
  4

• Legends cropped in multiQC results

  #123 opened a month ago by paulinefx
  0

• Create nf-core module for Cellbender background removal

  #110 opened a month ago by nictru
  0

• Create nf-core module for SCDS

  #118 opened a month ago by nictru
  0

• Allow doublet detection score calculation without actually removing doublets

  #106 opened a month ago by nictru
  0

• Create nf-core module for DecontX

  #113 opened a month ago by nictru
  0

• Implement gene regulatory network analyses

  #119 opened a month ago by nictru
  0

• Create nf-core module for Scrublet

  #116 opened a month ago by nictru
  0

• Move preprocessing modules to nf-core/modules

  #109 opened a month ago by nictru
  0

• Implement cell-cell interaction analyses

  #107 opened a month ago by nictru
  0

• MultiQC config not found

  #104 opened a month ago by marcus-tutert
  0

• Add MT percentage filtering

  #87 opened 2 months ago by nictru
  0

• Add support to Celltypist for non-human species.

  #98 opened 2 months ago by tbrittoborges
  0

• Add support for learning an scANVI model based on a given scVI model and cell type annotations

  #95 opened 3 months ago by nictru
  0

• Counts layer required for Scds and Solo is missing

  #91 opened 3 months ago by pakiessling
  0

• Pipeline not running correctly on GPU

  #90 opened 3 months ago by pakiessling
  5

• MultiQC fails with latest dev release

  #83 opened 3 months ago by alexblaessle
  0

• Minimal sample sheet with both filtered and unfiltered produced by scrnaseq triggers celda decontx runtime error

  #64 opened 3 months ago by smoe
  2

• Implement GPU support for relevant tools

  #69 opened 3 months ago by nictru
  4

• celltypist fails with value error

  #72 opened 3 months ago by fbnrst
  1

• additional output for cellbender

  #75 opened 3 months ago by fbnrst
  1

• CELDA_DECONTX - bails out over negative size factors

  #51 opened 4 months ago by smoe
  13

• AMBIENT_RNA_REMOVAL needs revision - runtime error ch_raw undefined with cellbender

  #65 opened 5 months ago by smoe
  0

• Add support for background matrix in `decontX`

  #57 opened 5 months ago by nictru
  0

• cellbender -> pytorch -> disk full, but it is not!

  #58 opened 5 months ago by smoe
  3

• cellbender needs raw count matrix as input

  #53 opened 5 months ago by fbnrst
  0

• Add support for h5 input format

  #48 opened 5 months ago by nictru
  1

• MPLCONFIGDIR expected in $HOME outside what singularity allows

  #49 opened 5 months ago by smoe
  2

• Implement cell type assignment methods

  #20 opened 6 months ago by nictru
  3

• Implement methods for ambient RNA removal

  #25 opened 6 months ago by nictru
  1

• Implement celltypist cell type assignment

  #21 opened 6 months ago by nictru
  0

• Implement scAR ambient RNA removal

  #31 opened 6 months ago by nictru
  2

• Implement soupX ambient RNA removal

  #26 opened 6 months ago by nictru
  0

• Implement cellbender ambient RNA removal

  #27 opened 6 months ago by nictru
  0

• Implement SCDS doublet detection

  #19 opened 6 months ago by nictru
  0

• Implement DoubletDetection doublet detection

  #16 opened 6 months ago by nictru
  0

• Implement DoubletDecon doublet detection

  #17 opened 6 months ago by nictru
  0

• Implement DoubletFinder doublet detection

  #18 opened 6 months ago by nictru
  0

• Add support for count matrices as pipeline input

  #29 opened 6 months ago by nictru
  0

• Implement SingleR cell type assignment

  #24 opened 6 months ago by nictru
  0

• Implement scPred cell type assignment

  #23 opened 6 months ago by nictru
  0

• Implement Azimuth cell type assignment

  #22 opened 6 months ago by nictru
  0