theislab/cellrank

Issues

• Problems with g.predict_terminal_states() and g.compute_fate_probabilities()

  #1209 opened 4 months ago by kathbosc
  5

• TypeError: Neighbors.compute_neighbors() got an unexpected keyword argument 'write_knn_indices'

  #1230 opened 2 months ago by hyjforesight
  2

• bone_marrow dataset is gone

  #1229 opened 2 months ago by hyjforesight
  1

• can i use cellrank2 on scrna dataset which which i have computed a pseudotime and vector filed using sctour?

  #1228 opened 2 months ago by JIMCAOWJ
  1

• consider add more visualization tool for CellRank2 meets with experimental timepoint (waddington transport)

  #1221 opened 2 months ago by LiuCanidk
  9

• Docs outdated

  #1226 opened 2 months ago by WeilerP
  0

• AttributeError: 'NoneType' object has no attribute 'gam'

  #1225 opened 2 months ago by kakarotcq
  1

• ValueError: Input matrix P is not a transition matrix.

  #1224 opened 2 months ago by Ferris01
  1

• AttributeError: 'csr_matrix' object has no attribute 'A' while calling plot_single_flow

  #1222 opened 2 months ago by WeihangChen0
  2

• References outdated

  #1218 opened 3 months ago by WeilerP
  0

• pl.log_odds() shows no figure

  #1216 opened 3 months ago by Alvis-Jiang
  1

• heatmap plot: what are the column

  #1195 opened 7 months ago by mxposed
  2

• plot_random_walks csr_matrix error

  #1213 opened 4 months ago by simozhou
  1

• Compute Transition Matrix Error CellRank Meets RNA Velocity

  #1211 opened 4 months ago by anthonyinsalaco1
  7

• Functsions related to Expression Trend not working

  #1207 opened 5 months ago by JyoRoy21
  1

• Question about metabolic labeling analysis

  #1208 opened 5 months ago by mingjianPeng
  6

• Pipeline from Seurat object to CellRank

  #1204 opened 5 months ago by mainharryHR
  4

• plot_single_flow raw data interpretation

  #1196 opened 5 months ago by fafa92
  1

• OSError when downloading example data: Unable to synchronously open file

  #1188 opened 5 months ago by LiuCanidk
  2

• ERROR: No .egg-info directory found when install with pip

  #1201 opened 5 months ago by FessenSimon
  1

• How to improve the accuracy for CytoTRACEKernel pipeline? Any parameter I can adjust?

  #1206 opened 5 months ago by mainharryHR
  6

• Errors for compute_transition_matrix

  #1205 opened 5 months ago by mainharryHR
  2

• Can key genes be identified?

  #1203 opened 5 months ago by GLking123
  2

• Compute and plot gene module scores over pseudotime

  #1202 opened 5 months ago by sohrabsa
  2

• unable to install cellrank

  #1200 opened 6 months ago by jchenpku
  1

• CellRank can't be used in Python versions >3.9

  #1199 opened 6 months ago by mpiersonsmela
  4

• Question about Transition Matrix and Initial States

  #1198 opened 7 months ago by jennylsmith
  1

• Extract gene expression on pseudotime from cellrank.pl.gene_trends

  #1197 opened 7 months ago by TinyTasy
  0

• ValueError: Transition matrix is not row stochastic, 8216 rows do not sum to 1.

  #1192 opened 7 months ago by simonekats
  13

• Manually adding a macrostate?

  #1193 opened 7 months ago by mxposed
  4

• A question about ‘g_fwd.compute_fate_probabilities(preconditioner='ilu', tol=1e-7, solver='direct')’

  #1194 opened 7 months ago by liuyang218622
  5

• gene expression trends line plots grouped by sample conditions

  #1191 opened 7 months ago by qinting
  1

• The order of row names of adata.obsm['lineages_fwd']

  #1190 opened 7 months ago by liuyang218622
  1

• Comparing conditions in cellrank

  #1181 opened 7 months ago by dyinboisry4u
  2

• Proper use of the "Lineages" Parameter for Lineage Drivers

  #1182 opened 8 months ago by jwalewski
  10

• 3D UMAP and RNA velocity matrices

  #1187 opened 8 months ago by fafa92
  2

• In cases the same cluster is estimated as initial and terminal states

  #1189 opened 7 months ago by st-tky
  4

• Simple cellrank 2 installation and loading error; scvelo compatibility

  #1186 opened 8 months ago by darrentyson
  1

• Update type hinting

  #1178 opened 8 months ago by WeilerP
  3

• Problem with plotting fate probabilities separately "'NoneType' object has no attribute '_get_renderer'"

  #1185 opened 8 months ago by azbukinanadezda
  5

• ImportError: cannot import name 'deprecated_arg_names' from 'scanpy._utils' since scanpy 1.10.0 release

  #1183 opened 8 months ago by Zethson
  6

• Cellrank - CytoTRACE Kernel with Harmony results

  #1180 opened 8 months ago by xiandxing
  1

• Plot states as in CellRank 2

  #1176 opened 8 months ago by WeilerP
  1

• Inverse-squared link error

  #1170 opened 9 months ago by loicguille
  5

• Cross-boundary correctness score

  #1167 opened 9 months ago by WeilerP
  0

• Test CI fail with `pytest==8.1.0`

  #1173 opened 9 months ago by WeilerP
  1

• Add terminal state identification score

  #1165 opened 9 months ago by WeilerP
  0

• beginner question: how to save figure by vk.plot_projection in PDF?

  #1171 opened 9 months ago by Roger-GOAT
  0

• Is there a way to remove the legend in cr.pl.gene_trends ?

  #1169 opened 9 months ago by t-nol
  1

• Ignore VS Code files

  #1163 opened 9 months ago by WeilerP
  0