theislab cellrank issues

theislab / cellrank

CellRank: dynamics from multi-view single-cell data

https://cellrank.org

BSD 3-Clause "New" or "Revised" License

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issues

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Calculation of transition matrix problem,ValueError: Input matrix P is not a transition matrix.

#1234 Angle28 opened 14 hours ago
3
AttributeError: module 'matplotlib.cbook' has no attribute 'mplDeprecation'

#1232 wzyfudan closed 2 weeks ago
3
Why not take scipy implementation of Pearson correlation for computing lineage drivers?

#1231 VladimirShitov opened 1 month ago
3
TypeError: Neighbors.compute_neighbors() got an unexpected keyword argument 'write_knn_indices'

#1230 hyjforesight closed 1 month ago
2
bone_marrow dataset is gone

#1229 hyjforesight closed 1 month ago
1
can i use cellrank2 on scrna dataset which which i have computed a pseudotime and vector filed using sctour?

#1228 JIMCAOWJ opened 1 month ago
1
Update docs

#1227 WeilerP closed 1 month ago
4
Docs outdated

#1226 WeilerP closed 1 month ago
0
AttributeError: 'NoneType' object has no attribute 'gam'

#1225 kakarotcq closed 2 months ago
1
ValueError: Input matrix P is not a transition matrix.

#1224 Ferris01 closed 2 months ago
1
Fix adata copy (coarse transition matrix)

#1223 michalk8 closed 2 months ago
0
AttributeError: 'csr_matrix' object has no attribute 'A' while calling plot_single_flow

#1222 WeihangChen0 closed 2 months ago
2
consider add more visualization tool for CellRank2 meets with experimental timepoint (waddington transport)

#1221 LiuCanidk closed 2 months ago
9
chore: bump ruff pre-commit hook version

#1220 afuetterer closed 2 months ago
2
Update references

#1219 WeilerP closed 2 months ago
1
References outdated

#1218 WeilerP closed 2 months ago
0
Update cellrank 2 paper citation

#1217 mxposed closed 2 months ago
2
pl.log_odds() shows no figure

#1216 Alvis-Jiang closed 2 months ago
1
Use `toarray()` instead of `.A`

#1214 michalk8 closed 3 months ago
0
plot_random_walks csr_matrix error

#1213 simozhou closed 3 months ago
1
Remove numba cache

#1212 michalk8 closed 3 months ago
0
Compute Transition Matrix Error CellRank Meets RNA Velocity

#1211 anthonyinsalaco1 closed 3 months ago
7
Problems with g.predict_terminal_states() and g.compute_fate_probabilities()

#1209 kathbosc closed 3 months ago
5
Question about metabolic labeling analysis

#1208 mingjianPeng closed 4 months ago
6
Functsions related to Expression Trend not working

#1207 JyoRoy21 opened 4 months ago
1
How to improve the accuracy for CytoTRACEKernel pipeline? Any parameter I can adjust?

#1206 mainharryHR closed 4 months ago
6
Errors for compute_transition_matrix

#1205 mainharryHR closed 4 months ago
2
Pipeline from Seurat object to CellRank

#1204 mainharryHR closed 4 months ago
4
Can key genes be identified?

#1203 GLking123 closed 4 months ago
2
Compute and plot gene module scores over pseudotime

#1202 sohrabsa opened 5 months ago
2
ERROR: No .egg-info directory found when install with pip

#1201 FessenSimon closed 4 months ago
1
unable to install cellrank

#1200 jchenpku closed 5 months ago
1
CellRank can't be used in Python versions >3.9

#1199 mpiersonsmela closed 5 months ago
4
Question about Transition Matrix and Initial States

#1198 jennylsmith opened 6 months ago
1
Extract gene expression on pseudotime from cellrank.pl.gene_trends

#1197 TinyTasy opened 6 months ago
0
plot_single_flow raw data interpretation

#1196 fafa92 closed 4 months ago
1
heatmap plot: what are the column

#1195 mxposed closed 6 months ago
2
A question about ‘g_fwd.compute_fate_probabilities(preconditioner='ilu', tol=1e-7, solver='direct')’

#1194 liuyang218622 opened 7 months ago
5
Manually adding a macrostate?

#1193 mxposed closed 7 months ago
4
ValueError: Transition matrix is not row stochastic, 8216 rows do not sum to 1.

#1192 simonekats opened 7 months ago
13
gene expression trends line plots grouped by sample conditions

#1191 qinting opened 7 months ago
1
The order of row names of adata.obsm['lineages_fwd']

#1190 liuyang218622 closed 7 months ago
1
In cases the same cluster is estimated as initial and terminal states

#1189 st-tky opened 7 months ago
4
OSError when downloading example data: Unable to synchronously open file

#1188 LiuCanidk closed 4 months ago
2
3D UMAP and RNA velocity matrices

#1187 fafa92 closed 7 months ago
2
Simple cellrank 2 installation and loading error; scvelo compatibility

#1186 darrentyson closed 7 months ago
1
Problem with plotting fate probabilities separately "'NoneType' object has no attribute '_get_renderer'"

#1185 azbukinanadezda closed 7 months ago
5
Fix/importError #1183

#1184 Abelgurung closed 7 months ago
1
ImportError: cannot import name 'deprecated_arg_names' from 'scanpy._utils' since scanpy 1.10.0 release

#1183 Zethson closed 7 months ago
6
Proper use of the "Lineages" Parameter for Lineage Drivers

#1182 jwalewski opened 7 months ago
10