Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
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
#1222 - AttributeError: 'csr_matrix' object has no attribute 'A' while calling plot_single_flow
Issue -
State: closed - Opened by WeihangChen0 18 days ago
- 1 comment
Labels: bug
#1221 - consider add more visualization tool for CellRank2 meets with experimental timepoint (waddington transport)
Issue -
State: open - Opened by LiuCanidk 21 days ago
- 1 comment
Labels: enhancement
#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#1218 - References outdated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
#1194 - A question about ‘g_fwd.compute_fate_probabilities(preconditioner='ilu', tol=1e-7, solver='direct')’
Issue -
State: open - Opened by liuyang218622 5 months ago
- 5 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
#1185 - Problem with plotting fate probabilities separately "'NoneType' object has no attribute '_get_renderer'"
Issue -
State: closed - Opened by azbukinanadezda 6 months ago
- 5 comments
Labels: bug
#1184 - Fix/importError #1183
Pull Request -
State: closed - Opened by Abelgurung 6 months ago
- 1 comment
#1183 - ImportError: cannot import name 'deprecated_arg_names' from 'scanpy._utils' since scanpy 1.10.0 release
Issue -
State: closed - Opened by Zethson 6 months ago
- 6 comments
Labels: bug
#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
#1131 - A question about g.predict_terminal_states(method="top_n", n_states=6) and g.plot_macrostates(which="terminal")
Issue -
State: closed - Opened by liuyang218622 12 months ago
- 2 comments
Labels: question
#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