kaizhang/SnapATAC2

Issues

• Handle BED headers in read_regions

  #384 opened 14 days ago by ofarrelle
  0

• MASC3 release 3.0.3

  #380 opened 14 days ago by aowenson-imm
  1

• clash with scipy 1.15.2

  #386 opened 14 days ago by dzhao98
  0

• Suggestions on discriminating mitosis cells (proliferative cells) from non-proliferative cells by snapatacv2.

  #385 opened 14 days ago by wangmeijiao
  1

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

  #348 opened 5 months ago by thecatsmilk
  6

• Error in integrated scRNA-seq data

  #383 opened 23 days ago by qingzengLi
  2

• Kernel crushed when running snap.pp.filter_cells

  #378 opened 23 days ago by linlejiang
  2

• Questions about snapatac2.pp.make_gene_matrix

  #382 opened a month ago by raywzr
  1

• Nan error in RNA-ATAC integration

  #381 opened a month ago by HOKYOUNGWWW
  0

• snapatac2.tl.macs3 command encountered an error using the call_broad_peaks function

  #379 opened a month ago by haloudashu
  0

• install snapatac2 error -- Failed to build snapatac2 MACS3

  #375 opened 2 months ago by hwa2Hu
  6

• `Memory allocation of bytes failed`

  #377 opened a month ago by nleroy917
  0

• Making AnnDataSet changes reflect in individual sample files

  #376 opened 2 months ago by anthonyinsalaco1
  2

• When installed SnapATAC2 in anaconda, it failed to progress to macs3. Please help me

  #374 opened 3 months ago by pi-0-pa
  2

• snap.pp.import_fragments import error

  #372 opened 3 months ago by bio-xtt
  4

• anaconda中安装snapATAC2会在macs3处报错

  #373 opened 3 months ago by pi-0-pa
  0

• Is there any parameters like batch for the function snapatac2.pp.scrublet？

  #371 opened 3 months ago by Jiang-Mengnan
  2

• Unable to edit backed AnnData

  #369 opened 4 months ago by jpmcga
  2

• Bug running harmony batch correction with multiple covariates

  #370 opened 3 months ago by joseverdezoto
  1

• bigwig normalization issue

  #366 opened 4 months ago by UCDNJJ
  27

• Calculation Method and Significance of "frac_confidently_mapped" ?

  #361 opened 4 months ago by haloudashu
  1

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

  #344 opened 4 months ago by joseverdezoto
  3

• stuck in snap.pp.scrublet(data）step

  #368 opened 4 months ago by junjunlab
  8

• diff_test get ValueError: Input X contains infinity or a value too large for dtype('float64').

  #364 opened 4 months ago by wkl1990
  4

• Could we provide more parameters for exporting bigwig files?

  #357 opened 4 months ago by beyondpie
  5

• Now to read .snap file using snapATAC2

  #367 opened 4 months ago by juychen
  1

• Feature Requeset: Add broadpeak support for single-cell cut&tag data?

  #365 opened 4 months ago by yxwucq
  2

• Failed to run peak calling function

  #363 opened 4 months ago by chengmingbo
  3

• bigwig normalization issue

  #360 opened 4 months ago by Salvacasani
  2

• Unexpected Abortion When Subsetting Data

  #349 opened 4 months ago by wkl1990
  1

• The value of 'Fraction of high-quality fragments overlapping peaks' is greater than 1

  #362 opened 4 months ago by haloudashu
  0

• Cannot compute joint embedding on RNA and ATAC object

  #350 opened 6 months ago by thecatsmilk
  4

• Order of the chromosomes

  #359 opened 5 months ago by HarveyYan
  2

• merge_peaks error

  #347 opened 5 months ago by caofan
  4

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

  #356 opened 5 months ago by mkarikom
  3

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

  #333 opened 5 months ago by jpmcga
  2

• function similar as Signac FilterCells

  #355 opened 5 months ago by Xieeeee
  1

• macs3 function not works with multiple dataset

  #332 opened 7 months ago by uqnsarke
  4

• Cannot process anndata's created from snapatac2.read_10x_mtx

  #352 opened 6 months ago by edward9065
  3

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

  #345 opened 6 months ago by newtonharry
  2

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

  #338 opened 6 months ago by yojetsharma
  3

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

  #343 opened 6 months ago by yojetsharma
  4

• 'make_fragment_file' is not working

  #334 opened 7 months ago by dahun73
  5

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

  #331 opened 7 months ago by beyondpie
  3

• Question about differential test

  #340 opened 6 months ago by beyondpie
  1

• snap.tl.macs3 error

  #336 opened 7 months ago by HaikuoLi
  5

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

  #337 opened 7 months ago by yojetsharma
  0

• Issue running snap.tl.macs3()

  #341 opened 6 months ago by thecatsmilk
  1

• 'make_gene_matrix' error for rat genome

  #335 opened 7 months ago by UCDNJJ
  5

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

  #330 opened 7 months ago by thecatsmilk
  10