Teichlab/celltypist

Issues

• Why we need to ensure the data format is adjusted with 10,000 for normalization correctness?

  #138 opened 3 months ago by HelloWorldLTY
  1

• Cluster level annotation question

  #137 opened 3 months ago by liuyang2006
  1

• Celltypist's MIT license and GPL dependency leidenalg

  #135 opened 3 months ago by PertuyF
  0

• cluster free annotation

  #134 opened 3 months ago by Flu09
  1

• Failure to install

  #133 opened 4 months ago by tricityandrew
  1

• AnnData Backed Mode Support

  #131 opened 4 months ago by kennypavan
  2

• SCT Object Compatibility with celltypist

  #132 opened 4 months ago by katkatrach
  2

• The full names of cell types

  #130 opened 4 months ago by BioAmelie
  0

• How can I subset the model to a select few cell types/clusters before training the model?

  #129 opened 5 months ago by yojetsharma
  6

• unable to download models

  #98 opened a year ago by mxiang1
  4

• celltypist before/after batch correction

  #119 opened 8 months ago by malonzm1
  10

• Running celltypist with concatenated dataset

  #106 opened 5 months ago by malonzm1
  4

• downsampling before training the model

  #128 opened 5 months ago by Flu09
  1

• Cell Typist Providing different results between iterations

  #126 opened 5 months ago by ManuelSokolov
  6

• multiple models

  #112 opened 9 months ago by anke-king
  7

• Is celltypist suitable for predicting mouse immune types？

  #127 opened 5 months ago by ttt-404
  1

• Cellxgene links offline

  #125 opened 5 months ago by canergen
  1

• Any reason why CellTypist is not part of scverse ecosystem?

  #123 opened 6 months ago by Rafael-Silva-Oliveira
  2

• sklearn version log/log_loss

  #124 opened 6 months ago by JAshcroft36
  1

• Issue with Offline Label Transfer

  #122 opened 7 months ago by macelik
  2

• Organ atlas Citing CellTypist. Automatic cell type harmonization and integr…

  #121 opened 7 months ago by noob000007
  1

• www.celltypist.org is down, cannot download models

  #116 opened 9 months ago by sztankatt
  3

• Issue accessing www.celltypist.org - 502 Bad Gateway

  #120 opened 8 months ago by lucygarner
  5

• Feature: Support Rapids-singlecell

  #110 opened 8 months ago by Intron7
  1

• ValueError in celltypist.annotate

  #108 opened 9 months ago by katecycho
  3

• the question about conf_score

  #102 opened 9 months ago by noob000007
  3

• Very low confidence score even though labels are correct

  #118 opened 9 months ago by mousepixels
  2

• Can not download the model

  #117 opened 9 months ago by Knight1995
  2

• Conflict with variable genes and model training

  #115 opened 9 months ago by mousepixels
  1

• Question about over_clustering and conf_score?

  #114 opened 9 months ago by sranbhor
  1

• Can not detect a neighborhood graph, will construct one before the over-clustering

  #111 opened 10 months ago by Sirin24
  1

• Use of metacells?

  #97 opened 9 months ago by andreahanel
  4

• is it available to generate model.pkl file from a marker gene list

  #109 opened 10 months ago by fnhe
  1

• Running the CellTypist training function celltypist.train on a subset of genes

  #107 opened a year ago by dkapadia612
  1

• " have completed preprocessing and cell clustering. "

  #100 opened a year ago by noob000007
  2

• Unable to allocate xxx GiB for an array with shape and data type float64

  #95 opened a year ago by zqxiao2001
  2

• Immune_All_Low - model training question

  #104 opened a year ago by NikicaJEa
  4

• Cluster-level label prediction

  #105 opened a year ago by pwwang
  1

• CellTypist_Immune_Reference_v2 question

  #103 opened a year ago by NikicaJEa
  2

• codes for harmonizing the cell labels

  #101 opened a year ago by YOU-k
  2

• Feature Request: Store freqs in annotation when majority_vote set to True

  #99 opened a year ago by eroell
  2

• Running `celltypist.annotate` with `min_prop` can't create "Heterogeneous" category

  #96 opened a year ago by DanScarc
  2

• Error running celltypist

  #86 opened a year ago by malonzm1
  10

• confidence score definition

  #91 opened a year ago by mjstrumillo
  2

• Using model trained by scRNA-seq datasets to predict Spatial transcriptmoic dataset

  #94 opened a year ago by SNOL2
  2

• Potentially misleading error when counts are not in expected range

  #89 opened a year ago by padix-key
  3

• Issues running with conda

  #92 opened a year ago by edridgedsouza
  3

• Request: allow to specify AnnData layer to use

  #90 opened a year ago by pcm32
  1

• Harmonize and Integrate

  #88 opened a year ago by YawnC
  1

• Allow to specify the AnnData var field that has the gene_symbols instead of only relying on var_names

  #87 opened a year ago by pcm32
  2