becavin-lab/checkatlas

Issues

• Implement metrics from Antoine Collin master thesis

  #48 opened 7 months ago by drbecavin
  0

• Add test datasets for spatial transcriptomics

  #47 opened 7 months ago by drbecavin
  0

• Spatial Image QC

  #46 opened 7 months ago by drbecavin
  0

• Tutorial for adding metrics in checklatlas

  #45 opened 7 months ago by drbecavin
  0

• Add test datasets

  #44 opened 7 months ago by drbecavin
  0

• Create github with all metrics

  #43 opened 7 months ago by drbecavin
  0

• Add multiomic singlce cell mangamenet

  #42 opened 7 months ago by drbecavin
  0

• Add SpatialData management

  #41 opened 7 months ago by drbecavin
  0

• Dimensionality reduction metrics

  #40 opened 7 months ago by drbecavin
  0

• Implement metrics from Malte Luecken's integration benchmark

  #39 opened 7 months ago by drbecavin
  0

• Write wiki/tutorial

  #15 opened a year ago by drbecavin
  1

• Seurat import

  #24 opened 2 years ago by drbecavin
  1

• QC figures does not display parameters for Seurat object

  #19 opened a year ago by drbecavin
  0

• Checkatlas conda, docker, singularity definition file

  #25 opened a year ago by drbecavin
  2

• Add management of information from integrated Atlas

  #16 opened a year ago by drbecavin
  0

• Automatic/Semi-automatic search of celltype key

  #13 opened a year ago by drbecavin
  0

• Add Kruskal stress calculation

  #9 opened a year ago by drbecavin
  0

• Problem of CPUs and ram utilization in multithread mode

  #14 opened a year ago by drbecavin
  0

• QC figures too big

  #12 opened a year ago by drbecavin
  0

• Multiome seurat object bad conversion

  #8 opened a year ago by drbecavin
  0

• Add knee plots

  #21 opened a year ago by grst
  5

• Improve Mito and ribo QC calculation

  #36 opened a year ago by drbecavin
  0

• Integration to scVerse

  #35 opened a year ago by drbecavin
  0

• Integration with nf-core pipelines

  #34 opened a year ago by grst
  5

• Dim reduction metric management for seurat object

  #27 opened 2 years ago by drbecavin
  0

• Fix parameters for checkatlas tools

  #11 opened 2 years ago by drbecavin
  1

• Umap with seurat_cluster does not display cluster

  #10 opened 2 years ago by drbecavin
  1

• Parse additional cellranger outputs

  #20 opened 2 years ago by chris-rands
  3

• Add Muon object

  #22 opened 2 years ago by drbecavin
  0

• Checkatlas .tsv tables in a separate folder

  #18 opened 3 years ago by drbecavin
  1

• Save table metrics

  #6 opened 3 years ago by drbecavin
  0

• Parse all features of an atlas

  #3 opened 3 years ago by drbecavin
  0

• Implement all metrics

  #5 opened 3 years ago by drbecavin
  0

• Implement metrics object

  #4 opened 3 years ago by drbecavin
  0

• Load and Convert Seurat atlas

  #1 opened 3 years ago by drbecavin
  0

• Load Scanpy object

  #2 opened 3 years ago by drbecavin
  0

• Create summary html with multiqc

  #7 opened 3 years ago by drbecavin
  1