Ecosyste.ms: Issues

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GitHub / theislab/cellrank issues and pull requests

#1223 - Fix adata copy (coarse transition matrix)

Pull Request - State: closed - Opened by michalk8 16 days ago
Labels: bugfix

#1220 - chore: bump ruff pre-commit hook version

Pull Request - State: closed - Opened by afuetterer 26 days ago - 1 comment

#1219 - Update references

Pull Request - State: closed - Opened by WeilerP 27 days ago - 1 comment

#1218 - References outdated

Issue - State: closed - Opened by WeilerP 27 days ago

#1217 - Update cellrank 2 paper citation

Pull Request - State: closed - Opened by mxposed about 1 month ago - 2 comments

#1216 - pl.log_odds() shows no figure

Issue - State: closed - Opened by Alvis-Jiang about 1 month ago - 1 comment
Labels: question

#1214 - Use `toarray()` instead of `.A`

Pull Request - State: closed - Opened by michalk8 about 2 months ago
Labels: bug

#1213 - plot_random_walks csr_matrix error

Issue - State: closed - Opened by simozhou about 2 months ago - 1 comment
Labels: bug

#1212 - Remove numba cache

Pull Request - State: closed - Opened by michalk8 about 2 months ago

#1211 - Compute Transition Matrix Error CellRank Meets RNA Velocity

Issue - State: closed - Opened by anthonyinsalaco1 3 months ago - 7 comments
Labels: bug

#1209 - Problems with g.predict_terminal_states() and g.compute_fate_probabilities()

Issue - State: closed - Opened by kathbosc 3 months ago - 4 comments
Labels: question

#1208 - Question about metabolic labeling analysis

Issue - State: closed - Opened by mingjianPeng 3 months ago - 6 comments
Labels: question

#1207 - Functsions related to Expression Trend not working

Issue - State: open - Opened by JyoRoy21 3 months ago - 1 comment
Labels: bug

#1206 - How to improve the accuracy for CytoTRACEKernel pipeline? Any parameter I can adjust?

Issue - State: closed - Opened by mainharryHR 3 months ago - 6 comments
Labels: question

#1205 - Errors for compute_transition_matrix

Issue - State: closed - Opened by mainharryHR 3 months ago - 2 comments
Labels: question

#1204 - Pipeline from Seurat object to CellRank

Issue - State: closed - Opened by mainharryHR 3 months ago - 4 comments
Labels: enhancement

#1203 - Can key genes be identified?

Issue - State: closed - Opened by GLking123 3 months ago - 2 comments
Labels: question

#1202 - Compute and plot gene module scores over pseudotime

Issue - State: open - Opened by sohrabsa 4 months ago - 2 comments
Labels: enhancement

#1201 - ERROR: No .egg-info directory found when install with pip

Issue - State: closed - Opened by FessenSimon 4 months ago - 1 comment
Labels: bug

#1200 - unable to install cellrank

Issue - State: closed - Opened by jchenpku 4 months ago - 1 comment
Labels: bug

#1199 - CellRank can't be used in Python versions >3.9

Issue - State: closed - Opened by mpiersonsmela 4 months ago - 4 comments
Labels: bug

#1198 - Question about Transition Matrix and Initial States

Issue - State: open - Opened by jennylsmith 5 months ago - 1 comment
Labels: question

#1197 - Extract gene expression on pseudotime from cellrank.pl.gene_trends

Issue - State: open - Opened by TinyTasy 5 months ago
Labels: question

#1196 - plot_single_flow raw data interpretation

Issue - State: closed - Opened by fafa92 5 months ago - 1 comment
Labels: question

#1195 - heatmap plot: what are the column

Issue - State: closed - Opened by mxposed 5 months ago - 2 comments
Labels: question

#1193 - Manually adding a macrostate?

Issue - State: closed - Opened by mxposed 5 months ago - 4 comments
Labels: question

#1192 - ValueError: Transition matrix is not row stochastic, 8216 rows do not sum to 1.

Issue - State: open - Opened by simonekats 5 months ago - 13 comments
Labels: bug

#1191 - gene expression trends line plots grouped by sample conditions

Issue - State: open - Opened by qinting 5 months ago - 1 comment
Labels: question

#1190 - The order of row names of adata.obsm['lineages_fwd']

Issue - State: closed - Opened by liuyang218622 5 months ago - 1 comment
Labels: question

#1189 - In cases the same cluster is estimated as initial and terminal states

Issue - State: open - Opened by st-tky 6 months ago - 4 comments
Labels: question

#1188 - OSError when downloading example data: Unable to synchronously open file

Issue - State: closed - Opened by LiuCanidk 6 months ago - 2 comments
Labels: bug

#1187 - 3D UMAP and RNA velocity matrices

Issue - State: closed - Opened by fafa92 6 months ago - 2 comments
Labels: question

#1186 - Simple cellrank 2 installation and loading error; scvelo compatibility

Issue - State: closed - Opened by darrentyson 6 months ago - 1 comment
Labels: bug

#1184 - Fix/importError #1183

Pull Request - State: closed - Opened by Abelgurung 6 months ago - 1 comment

#1182 - Proper use of the "Lineages" Parameter for Lineage Drivers

Issue - State: open - Opened by jwalewski 6 months ago - 10 comments
Labels: question

#1181 - Comparing conditions in cellrank

Issue - State: closed - Opened by dyinboisry4u 6 months ago - 2 comments
Labels: question

#1180 - Cellrank - CytoTRACE Kernel with Harmony results

Issue - State: closed - Opened by xiandxing 6 months ago - 1 comment
Labels: question

#1178 - Update type hinting

Issue - State: open - Opened by WeilerP 6 months ago - 3 comments

#1177 - Update state plotting

Pull Request - State: closed - Opened by WeilerP 7 months ago - 1 comment

#1176 - Plot states as in CellRank 2

Issue - State: closed - Opened by WeilerP 7 months ago - 1 comment
Labels: enhancement

#1175 - Update pyGAM link function

Pull Request - State: closed - Opened by WeilerP 7 months ago - 1 comment

#1174 - Fix/tsi unsetting

Pull Request - State: closed - Opened by michalk8 7 months ago - 1 comment

#1173 - Test CI fail with `pytest==8.1.0`

Issue - State: open - Opened by WeilerP 7 months ago - 1 comment

#1172 - Update `pyproject`

Pull Request - State: closed - Opened by WeilerP 7 months ago - 1 comment

#1171 - beginner question: how to save figure by vk.plot_projection in PDF?

Issue - State: closed - Opened by Roger-GOAT 7 months ago
Labels: enhancement

#1170 - Inverse-squared link error

Issue - State: closed - Opened by loicguille 7 months ago - 5 comments
Labels: question

#1169 - Is there a way to remove the legend in cr.pl.gene_trends ?

Issue - State: closed - Opened by t-nol 7 months ago - 1 comment
Labels: question

#1168 - Add CBC score

Pull Request - State: closed - Opened by WeilerP 7 months ago - 2 comments

#1167 - Cross-boundary correctness score

Issue - State: closed - Opened by WeilerP 7 months ago
Labels: enhancement

#1166 - Add TSI score code

Pull Request - State: closed - Opened by WeilerP 7 months ago - 4 comments

#1165 - Add terminal state identification score

Issue - State: closed - Opened by WeilerP 7 months ago
Labels: enhancement

#1164 - Update `.gitignore`

Pull Request - State: closed - Opened by WeilerP 7 months ago

#1163 - Ignore VS Code files

Issue - State: closed - Opened by WeilerP 7 months ago
Labels: enhancement

#1162 - Update `heatmap`

Pull Request - State: closed - Opened by WeilerP 7 months ago - 2 comments
Labels: misc

#1161 - Check that genes to plot in heatmap exist

Issue - State: closed - Opened by WeilerP 7 months ago
Labels: bug

#1160 - Update `heatmap`

Pull Request - State: closed - Opened by WeilerP 7 months ago - 1 comment

#1159 - Heatmap title

Issue - State: closed - Opened by WeilerP 7 months ago
Labels: enhancement

#1158 - vk.compute_transition_matrix() gives zero-size array to reduction operation not possible

Issue - State: closed - Opened by leahrosen 8 months ago - 3 comments
Labels: bug

#1157 - applying Cytotrace to samples with different depth of coverage

Issue - State: closed - Opened by jlmalin 8 months ago - 2 comments
Labels: question

#1156 - Update issue templates

Pull Request - State: closed - Opened by Marius1311 8 months ago - 3 comments

#1155 - Enrichment analysis with pearson correlations

Issue - State: closed - Opened by TdzBAS 8 months ago - 4 comments
Labels: question

#1154 - Why are my fate probabilities so low in the heatmap?

Issue - State: closed - Opened by TdzBAS 8 months ago - 5 comments
Labels: question

#1153 - Compatibility problems with python >=3.10

Issue - State: closed - Opened by PaMartini 8 months ago - 2 comments

#1152 - BaseModel.prepare() unexpected behaviour

Issue - State: open - Opened by nrclaudio 9 months ago - 2 comments
Labels: bug

#1151 - Available GPU support in CellRank 2?

Issue - State: closed - Opened by zvittorio 9 months ago - 3 comments
Labels: question

#1150 - A question about cr.pl.circular_projection parameter "normalize_by_mean"

Issue - State: closed - Opened by yulicarp 9 months ago - 2 comments
Labels: question

#1149 - Where to find the old tutorials?

Issue - State: closed - Opened by hyjforesight 9 months ago - 2 comments
Labels: question

#1148 - Segfault / python free() invalid size error during compute_transition_matrix

Issue - State: open - Opened by KforKuma 9 months ago - 5 comments
Labels: bug

#1147 - How to Combine Seurat AnnData and VeloCyto AnnData

Issue - State: closed - Opened by jwalewski 10 months ago - 2 comments
Labels: question

#1146 - RealTimeKernel.from_moscot(tp) Out of Memory

Issue - State: open - Opened by AlinaKurjan 10 months ago - 27 comments
Labels: question

#1145 - How to get differential kinetics

Issue - State: closed - Opened by roskcl 10 months ago - 2 comments

#1144 - Function not found

Issue - State: closed - Opened by SevenTea7 10 months ago - 1 comment

#1143 - Remove matplotlib upper pin from

Pull Request - State: closed - Opened by michalk8 10 months ago

#1142 - pk.plot_random_walks → AttributeError: can't set attribute"

Issue - State: closed - Opened by singlece 10 months ago - 2 comments
Labels: bug

#1140 - Plotting issue with `cellrank`

Issue - State: closed - Opened by cartal 11 months ago - 1 comment
Labels: bug, question

#1139 - Compatibility with newest Mac hardware/software or Python version?

Issue - State: closed - Opened by YitengDang 11 months ago - 1 comment
Labels: bug

#1138 - Use new PyPI trusted publisher management

Pull Request - State: closed - Opened by michalk8 11 months ago

#1137 - AttributeError: module 'cellrank' has no attribute 'kernels'

Issue - State: closed - Opened by jwalewski 11 months ago - 10 comments
Labels: bug

#1136 - Fix pandas/PETSc issues

Pull Request - State: closed - Opened by michalk8 11 months ago - 1 comment
Labels: bug

#1135 - RuntimeError: No coarse-grained stationary distribution found

Issue - State: open - Opened by xyxuq 11 months ago - 6 comments
Labels: question

#1134 - petsc4py error when running "compute_fate_probabilities"

Issue - State: closed - Opened by miktrinh 11 months ago - 4 comments
Labels: bug

#1133 - Saving vk.plot_projection()

Issue - State: closed - Opened by JuliaChristiaanse 12 months ago - 3 comments
Labels: question

#1132 - expose pygam model penalties via spline_kwargs fixes #1126

Pull Request - State: closed - Opened by bfurtwa 12 months ago - 1 comment

#1130 - A question about cr.pl.gene_trends() of cellrank

Issue - State: closed - Opened by liuyang218622 12 months ago - 17 comments
Labels: question

#1129 - Using Seurat SNN graph in place of connectivities matrix

Issue - State: closed - Opened by WesleyRosales about 1 year ago - 2 comments
Labels: question

#1128 - Fix `pandas>=2.1.1`

Issue - State: closed - Opened by michalk8 about 1 year ago - 1 comment
Labels: bug

#1127 - Heatmap expression cascade enriched for genes peaking in most terminal state of the lineage

Issue - State: closed - Opened by reneemoerkens about 1 year ago - 7 comments
Labels: question

#1126 - Remove L2 penalty from pygam models

Issue - State: closed - Opened by bfurtwa about 1 year ago - 1 comment
Labels: enhancement

#1125 - Fix minor typos

Pull Request - State: closed - Opened by omahs about 1 year ago - 1 comment

#1124 - Saving figures generated by ScVelo and CellRank

Issue - State: closed - Opened by jwalewski about 1 year ago - 10 comments
Labels: enhancement

#1123 - Real Schur Decomposition High Values

Issue - State: closed - Opened by AlinaKurjan about 1 year ago - 2 comments
Labels: question

#1122 - Fix/anndata serialization

Pull Request - State: closed - Opened by michalk8 about 1 year ago - 1 comment
Labels: bugfix

#1121 - Tolerance not exposed

Issue - State: closed - Opened by Marius1311 about 1 year ago - 1 comment
Labels: question

#1120 - P-value for cellrank.pl.log_odds

Issue - State: closed - Opened by mcclo about 1 year ago - 2 comments
Labels: question