sib-swiss/single-cell-training

Issues

• Error in validObject(.Object) : invalid class “LogMap” object: superclass "mMatrix" not defined in the environment of the object's class

  #78 opened 4 months ago by shameem356
  1

• https://sib-swiss.github.io/single-cell-training/latest/ is offline

  #76 opened 4 months ago by vmkalbskopf
  3

• Set up quarto to run as action

  #74 opened 6 months ago by GeertvanGeest
  0

• Update overview of class Seurat object with v5

  #56 opened 6 months ago by taniawyss
  1

• Simplify pseudobulk analysis

  #63 opened a year ago by GeertvanGeest
  0

• Do integration based on layers

  #58 opened a year ago by GeertvanGeest
  1

• Bug monocle3 at step "cluster_cells"

  #48 opened a year ago by taniawyss
  2

• GetAssayData() slot argument deprecated

  #54 opened a year ago by taniawyss
  1

• Trajectory analysis - Monocle3 update access to counts

  #62 opened a year ago by taniawyss
  0

• update Docker build and push actions

  #59 opened a year ago by GeertvanGeest
  0

• AddModuleScore() needs a fix in Seurat v5

  #55 opened a year ago by taniawyss
  1

• Create a CITATION.cff

  #50 opened a year ago by GeertvanGeest
  0

• Update link to OrgDbs in Day 3 - Enrichment analysis

  #47 opened a year ago by taniawyss
  0

• Update links of day3 - Differential gene expression

  #46 opened a year ago by taniawyss
  0

• IGKC is nice

  #33 opened a year ago by jeitziner
  5

• Scaling all genes - necessary?

  #45 opened a year ago by GeertvanGeest
  1

• Add image as a resource

  #18 opened 2 years ago by GeertvanGeest
  2

• Package `Matrix` not in the right version

  #41 opened 2 years ago by GeertvanGeest
  2

• Package `org.Hs.eg.db` missing

  #42 opened 2 years ago by GeertvanGeest
  1

• Align teaching with this paper

  #19 opened 2 years ago by GeertvanGeest
  1

• Monocle3 not installed

  #25 opened 2 years ago by GeertvanGeest
  2

• Moncole 3 part does not work well in hosted container

  #27 opened 2 years ago by GeertvanGeest
  1

• Running cellranger

  #30 opened 2 years ago by GeertvanGeest
  1

• Error message in LabelPoint

  #31 opened 2 years ago by jeitziner
  1

• Make a time schedule for the course

  #37 opened 2 years ago by GeertvanGeest
  1

• Consider home work assignments

  #38 opened 2 years ago by GeertvanGeest
  1

• typo in cell annotation exercise

  #34 opened 2 years ago by taniawyss
  0

• add regression out to scaling and normalization

  #28 opened 2 years ago by GeertvanGeest
  1

• Do ora on pseudobulk

  #24 opened 2 years ago by GeertvanGeest
  0

• Add BD rhapsody to overview?

  #22 opened 2 years ago by GeertvanGeest
  2

• Add overview of different analysis packages

  #15 opened 2 years ago by GeertvanGeest
  0

• Use cell and feature filtering

  #7 opened 2 years ago by GeertvanGeest
  1

• Course data generation

  #14 opened 2 years ago by GeertvanGeest
  0

• consider sctk qc

  #17 opened 2 years ago by GeertvanGeest
  1

• Add `scater` to the Dockerfile

  #12 opened 2 years ago by GeertvanGeest
  0

• Add acknowledgements

  #10 opened 2 years ago by GeertvanGeest
  1

• Standardize the number of PCs

  #8 opened 2 years ago by GeertvanGeest
  0

• No NA in singleR annotation

  #13 opened 2 years ago by GeertvanGeest
  0

• Re-evaluate learning outcomes

  #9 opened 2 years ago by GeertvanGeest
  1

• Shared data in `/data`

  #16 opened 2 years ago by GeertvanGeest
  0

• Generate auto extracted code by gh action

  #21 opened 2 years ago by GeertvanGeest
  1

• add code singleR QC

  #1 opened 3 years ago by taniawyss
  0