kaizhang/SnapATAC2

Issues

• Downstream analysis tutorial

  #319 opened a month ago by GaF123
  2

• Annotation of differentially accessible peaks

  #299 opened 3 months ago by ayavuzcakir
  2

• Vignette for downstream analysis tools?

  #315 opened 2 months ago by zrlewis
  3

• snap.pp.import_data results in RuntimeError: H5Fcreate(): unable to create file: unable to truncate a file which is already open

  #317 opened 2 months ago by wgao688
  1

• How does one import multiple fragments.tsv.gz files from different samples?

  #314 opened 2 months ago by yojetsharma
  2

• Maintaining Batch Correction in Joint Embedding

  #311 opened 2 months ago by meiiemg
  1

• The analysis about non-single cell sequencing

  #313 opened 2 months ago by allanlinzhang
  1

• Extracting fragment count matrix

  #316 opened 2 months ago by lf96abc
  1

• Can't download pbmc10k_multiome

  #309 opened 2 months ago by Li-ZhiD
  1

• Unexpected behavior in AnnDataSet subset

  #310 opened 2 months ago by mtvector
  0

• Specify that all features are used if sample_size is None

  #307 opened 3 months ago by newtonharry
  0

• snapatac2.tl.diff_test

  #306 opened 3 months ago by TingTingShao
  2

• `TypeError: fork_exec() takes exactly 23 arguments (17 given)`

  #305 opened 4 months ago by nleroy917
  3

• How to calculate TSS(UP 1K,DOWN 1K) score for gene of every cell?

  #304 opened 4 months ago by mengchengyao
  3

• snap.pp.import_data hangs on 0%

  #302 opened 4 months ago by MubasherMohammed
  3

• Accessing and plotting QC metrics after merging to AnnDataSet: more documentation needed

  #300 opened 4 months ago by jeremymsimon
  1

• Bug: barcode_regex="(..:..:..:..):w+$" shown in the document

  #301 opened 4 months ago by beyondpie
  0

• Error related to parallelism when running `snap.tl.macs3` when running on the cluster

  #298 opened 5 months ago by PauBadiaM
  2

• cell number decreased significantly after loading to snapatac as h5ad file

  #296 opened 5 months ago by TingTingShao
  3

• snap.tl.macs3

  #297 opened 5 months ago by TingTingShao
  0

• snap.pp.mnc_correct groupby

  #292 opened 5 months ago by TingTingShao
  1

• AnnData subset function: out cannot be None.

  #251 opened 5 months ago by beyondpie
  10

• lots of integers in the python REPL during running spectral embedding

  #291 opened 5 months ago by beyondpie
  5

• hard to understand about the description in filter features.

  #290 opened 5 months ago by beyondpie
  1

• make_fragment_file output file is empty

  #288 opened 5 months ago by MaoxuWang
  2

• AnnDataSet loses the .obsm

  #287 opened 5 months ago by wgao688
  1

• make_gene_matrix: cannot set n_obs unless n_obs == 0

  #289 opened 5 months ago by wgao688
  3

• add_cor_scores

  #286 opened 5 months ago by TingTingShao
  2

• Cannot find macs2

  #283 opened 5 months ago by RuiyuRayWang
  2

• scanpy AnnData to snapatac2 AnnData: cannot read csr_matrix

  #276 opened 5 months ago by beyondpie
  2

• write anndataset

  #258 opened 5 months ago by TingTingShao
  5

• save images

  #275 opened 5 months ago by TingTingShao
  3

• trouble with pbmc notebook

  #277 opened 5 months ago by vjcitn
  4

• obs_names resets to original barcodes when assigned via AnnDataset

  #278 opened 5 months ago by newtonharry
  0

• Read bam with split reads

  #259 opened 6 months ago by lauradmartens
  5

• import data

  #269 opened 6 months ago by TingTingShao
  4

• info lost after converting anndataset into anndata

  #271 opened 6 months ago by TingTingShao
  2

• color by accessibility of a certain region

  #270 opened 6 months ago by TingTingShao
  0

• AnnDataSet overwritten

  #261 opened 6 months ago by TingTingShao
  5

• [Question from Beginner] How can I use SnapATAC2 if I don't have BAM file or fragment files?

  #265 opened 6 months ago by JiehoonKwak
  1

• Integration with SCENICplus

  #262 opened 6 months ago by TingTingShao
  0

• try different knn methods

  #264 opened 6 months ago by TingTingShao
  1

• SnapATAC2 Docker Image Pushed to Docker Hub

  #263 opened 6 months ago by dtgz-sudo
  0

• add_cor_scores could only selects capitalized genes?

  #260 opened 6 months ago by zkcao
  1

• snakemake workflow

  #256 opened 6 months ago by TingTingShao
  5

• Analysis of single-cell dataset that includes both single- and paired-end samples?

  #250 opened 6 months ago by zhang-jiankun
  1

• Too much time for snap.tl.spectral

  #252 opened 6 months ago by yuanlizhanshi
  4

• import_data() got multiple values for argument 'chrom_sizes'

  #255 opened 6 months ago by TingTingShao
  1

• Multi-sample modality pipeline QC

  #253 opened 6 months ago by TingTingShao
  3

• Installation Failed : M1 Pro, macOS Sonoma 14.3 (cannot install v2.5.3 or v.2.6.0)

  #248 opened 6 months ago by JiehoonKwak
  3