kaizhang/SnapATAC2

Issues

• Could we provide more parameters for exporting bigwig files?

  #357 opened 13 days ago
  5

• import_data(mybedfile.bed, ...) produces an adata with shape()==N x 0

  #356 opened 5 days ago
  3

• function similar as Signac FilterCells

  #355 opened 10 days ago
  1

• Cannot process anndata's created from snapatac2.read_10x_mtx

  #352 opened 23 days ago
  3

• Cannot compute joint embedding on RNA and ATAC object

  #350 opened 25 days ago
  3

• Unexpected Abortion When Subsetting Data

  #349 opened 25 days ago
  1

• Pull AnnDataSet matrix to integrate with scRNA-seq data, move to R

  #348 opened 13 days ago
  4

• merge_peaks error

  #347 opened 5 days ago
  4

• Total counts differs between different binning resolutions for the same chromosome

  #345 opened a month ago
  2

• Saving raw h5ad files upon running snap.pp.import_data

  #344 opened a month ago
  3

• [Multi modality pipeline] Are number of cells and var attributes required to be the same while performing rna atac embedding?

  #343 opened a month ago
  4

• Issue running snap.tl.macs3()

  #341 opened 2 months ago
  1

• Question about differential test

  #340 opened 2 months ago
  1

• ZeroDivisionError specific to snapatac2 pipeline or incompatability issue with scvi-tools?

  #338 opened a month ago
  3

• Is there a way generate a coverage plot for DARs?

  #337 opened 2 months ago
  0

• snap.tl.macs3 error

  #336 opened 2 months ago
  5

• 'make_gene_matrix' error for rat genome

  #335 opened 2 months ago
  5

• 'make_fragment_file' is not working

  #334 opened 2 months ago
  5

• tl.mac3 parameter 'store_bdg' in documentation for 2.7.0 but not actually in function

  #333 opened 10 days ago
  2

• macs3 function not works with multiple dataset

  #332 opened 2 months ago
  4

• AnnDataSet can not be converted to AnnData when the X is empty

  #331 opened 2 months ago
  3

• snap.pp.import_data() not working for fragments.tsv.gz files from cellranger-arc count

  #330 opened 2 months ago
  10

• Read .snap file

  #328 opened 2 months ago
  2

• Loading multiple h5ad files for annotation

  #327 opened 2 months ago
  11

• Label Transfer Using the SCVI-tools

  #326 opened 2 months ago
  1

• Is an RNA modality file from multiome needed/necessary to annotate clusters in scATAC dataset?

  #323 opened a month ago
  4

• ImportError Post-Installation

  #322 opened 2 months ago
  2

• Reproduce 10X cellrange QC metrics

  #321 opened 2 months ago
  1