broadinstitute wot issues

broadinstitute / wot

A software package for analyzing snapshots of developmental processes

https://broadinstitute.github.io/wot/

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

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issues

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

#108 WeihangChen0 closed 2 months ago
0
Calculating minimum transport distance between cells without time information

#107 Hilarialy opened 7 months ago
0
Error in visualizing trajectory

#106 hanjun98 opened 1 year ago
3
Error in visualizing trajectory

#105 Kei-kamo closed 1 year ago
3
Some questions about normalization

#104 809825706 opened 2 years ago
0
Overflow encountered in duality gap computation, please report this incident

#103 davhum opened 2 years ago
0
Avoid computing PCA when using a custom cost matrix

#102 matthieuheitz opened 2 years ago
0
Differential expression across different timepoints and fates forward in time

#101 matthieuheitz opened 2 years ago
0
Are all genes or highly variable genes used as input expression matrix in Waddington-OT?

#100 Mingsenli opened 2 years ago
1
How to adjust raw data to this format

#99 tar-art opened 2 years ago
1
Can't replicate data preprocessing

#98 morphy380 opened 2 years ago
2
pg.neighbors(adata_var) error

#97 noobugs opened 2 years ago
2
cell_growth_rates not passed on command line

#96 MikeDMorgan opened 3 years ago
0
Simplify updating `ot_configs`

#95 WeilerP opened 3 years ago
0
`wot.ot.OTModel` does not fail with random arguments

#94 WeilerP opened 3 years ago
0
Error met when running Notebook-1-FLE-cell_sets-gene_sets.ipynb

#93 WBY20 opened 3 years ago
0
replacing real time with pseudotime

#92 Alexgr97 opened 3 years ago
0
WOT integration as an external kernel in CellRank

#91 Marius1311 closed 3 years ago
12
Overflow warnings

#90 ShouWenWang opened 3 years ago
5
What is the difference between fate probability and ancestor probability?

#89 jma1991 opened 3 years ago
1
Reading mtx file

#88 hiraksarkar opened 3 years ago
1
Preparation of expression matrix

#87 jma1991 opened 3 years ago
4
Custom Cost Matrices

#86 Jabbath closed 4 years ago
0
Interpreting WOT ancestors and trajectory probabilities

#85 dkeitley closed 3 years ago
0
where to choose number of PCA to compute transport map?

#84 hahia closed 4 years ago
3
FutureWarning frome anndata

#83 hahia opened 4 years ago
0
'AnnData' object has no attribute 'to_anndata'

#82 hahia closed 4 years ago
3
error in wot.tmap.TransportMapModel.from_directory(TMAP_PATH)

#81 rosshandler closed 4 years ago
10
ExprMatrix.h5ad file

#80 sunliang3361 opened 4 years ago
0
Overflow encountered in duality gap computation

#79 alyosama closed 4 years ago
2
Using wot on scATAC data?

#78 smanne07 opened 4 years ago
2
problem on install wot

#77 llx174 opened 4 years ago
1
'cells_by_gene_set' - all cell types have the same number of cells

#76 mbk0asis closed 4 years ago
1
Composing couplings and transport maps explanations

#75 pausrrls opened 4 years ago
0
"Download tutorial input data" cannot be found

#74 ShouWenWang closed 5 years ago
1
duality_gap overflow

#73 MikeDMorgan closed 5 years ago
6
diff_exp not working after updating wot

#72 rosshandler opened 5 years ago
9
wot: error: argument command: invalid choice: 'neighborhood_graph'

#71 mbk0asis closed 4 years ago
6
I can't install

#70 wodanaz opened 5 years ago
5
Use of Timepoint Metadata

#69 jogiles opened 5 years ago
3
Modify read_anndata to read cellranger v3 matrices

#68 gabprg closed 5 years ago
2
Read dataset from 10x h5 file

#67 Huang-XN closed 5 years ago
1
create new cell sets in notebook 1

#66 yeroslaviz opened 5 years ago
0
trajectories fail except from final time point

#65 concatenize closed 5 years ago
1
trajectory plots unidentifiable.

#64 yeroslaviz opened 5 years ago
2
tmap_model.trajectories fails with two time points

#63 concatenize closed 5 years ago
1
calculting trajectories gives a warning "Variable names are not unique"

#62 yeroslaviz closed 5 years ago
1
error calculating gene_set scores "IndexError: tuple index out of range"

#61 yeroslaviz closed 5 years ago
1
import error "from scipy.sparse.sputils import IndexMixin"

#60 yeroslaviz opened 5 years ago
1
Installation error on MacOSX

#59 ghoshal closed 5 years ago
5