issues
search
aertslab
/
pycisTopic
pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
Other
58
stars
12
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
find_diff_features
#133
TingTingShao
closed
7 months ago
0
dimensionality reduction dictionary
#132
TingTingShao
closed
7 months ago
1
cistopic_obj has unexpected more nuclei number
#131
TingTingShao
closed
7 months ago
8
create_cistopic_object_from_fragments: numpy.core._exceptions._ArrayMemoryError [PERFORMANCE]
#130
DmitriiSeverinov
closed
7 months ago
3
pycisTopic.clust_vis.cell_topic_heatmap
#129
TingTingShao
closed
7 months ago
7
linux installation error
#128
kakaisi
opened
7 months ago
1
cell_topic_heatmap has argument "color_dict" but inside function it expects "color_dictionary"
#127
mrichter23
closed
7 months ago
0
compute_qc_stats
#126
TingTingShao
closed
7 months ago
3
cannot import name 'Self' from 'typing'
#125
TingTingShao
closed
7 months ago
2
NameError: name 'subset_list' is not defined
#124
w1973145618
opened
7 months ago
1
NameError: name 'Tuple' is not defined
#123
w1973145618
opened
8 months ago
3
CalledProcessError: Command '['/home/taxue/mywork/pycisTopic/Mallet-202108/bin/mallet', 'import-file', '--preserve-case', '--keep-sequence', '--token-regex', '\\S+', '--input', './scratch/leuven/330/vsc33053/ray_spill/mallet/tutorial/corpus.txt', '--output', './scratch/leuven/330/vsc33053/ray_spill/mallet/tutorial/corpus.mallet']' returned non-zero exit status 127.Bug report [BUG]
#121
w1973145618
opened
8 months ago
1
QC Based on Nucleosome Signal?
#118
salwanbutrus
closed
8 months ago
0
export_pseudobulk never generates pseudobulk files
#117
SITRR
opened
8 months ago
14
Performance optimisation request [PERFORMANCE]
#115
TingTingShao
closed
8 months ago
0
Topics has been calculated to number 350, but the loglikelihood is still not optimal.
#114
YH-Zheng
opened
8 months ago
3
Where can I find the "MO_GEX_seurat_Cortex.loom" file used in the multiple multiome tutorial?
#113
mossconfuse
opened
8 months ago
1
Merge master polars
#112
SeppeDeWinter
closed
9 months ago
0
Merge master in polars branch. Polars branch will become the new master branch in the future.
#111
SeppeDeWinter
closed
9 months ago
0
Unable to run pbmc tutorial ( export_pseudobulk)Bug report [BUG]
#109
Tu4n-ph4m
closed
9 months ago
1
import export_pseudobulk [ERROR]
#108
cbiagii
closed
9 months ago
3
Running pycisTopic on very large datasets [PERFORMANCE]
#106
simozhou
opened
10 months ago
14
Improve create pseudobulk
#105
SeppeDeWinter
closed
10 months ago
0
export_pseudobulk "Dataframe object has no attribute 'chromosomes'
#104
bhhlee
closed
9 months ago
4
export_pseudobulk not saving bed/bw files, and not printing "done!" message
#103
AmosFong1
closed
5 months ago
1
Bug report [BUG]
#102
Constantine-mty
closed
1 year ago
0
Create a cistopic object using ATAC-seq count matrix (peak by cell)?
#101
CYorick
opened
1 year ago
2
Error when running plot_topic() - `Unable to determine Axes to steal space for Colorbar`
#99
solvi808
opened
1 year ago
0
How to define "atac_anndata" in the toturial ??
#97
bitcometz
closed
1 year ago
0
pass use_polars parameter to funciton
#96
SeppeDeWinter
closed
1 year ago
0
find_diff_features Errors
#95
bitcometz
closed
1 year ago
2
Numba ConstantInferenceError in find_diff_features [BUG]
#94
josephineyates
opened
1 year ago
7
Bug report [Error with Ray while running pseudobulk_peak_calling]
#93
lila167
closed
1 year ago
3
run_umap errors [BUG]
#92
jklvrt
opened
1 year ago
5
Bug report [BUG]
#91
TomVuod
opened
1 year ago
2
`valid_bc` argument for `barcode_rank_function` has unanticipated behavior
#90
adamklie
closed
1 year ago
5
export_pseudobulk runs correctly but does not write "done!" for one cluster
#89
massonix
closed
1 year ago
3
:fire: add chromosome scaffold filtering
#88
mbuttner
opened
1 year ago
0
Add umap into cisTopic object?
#85
zhangqc723
closed
1 year ago
0
Issue with run_cgs_models_mallet [BUG - but maybe not directly pycistopic?]
#84
dagarfield
closed
1 year ago
2
TypeError: 'NoneType' object does not support item assignment - binarize_topics() function
#83
Sebdumas
opened
1 year ago
5
Tutorial for scATAC, when you also have scRNA-seq data but not in multiomics
#82
MariaRosariaNucera
closed
1 year ago
0
ValueError: Cannot convert float NaN to integer for compute_qc_stats from pycisTopic.qc
#81
orian116
closed
1 year ago
13
Ray processes failed to startup
#80
crsky1023
opened
1 year ago
5
Bug report [BUG] AttributeError: module 'numpy' has no attribute 'int' group_pr.to_bigwig
#79
etiennedanis
opened
1 year ago
2
Improve memory usage of "find_diff_features" and "markers" when using…
#78
ghuls
closed
1 year ago
2
Optimize memory usage of impute_accessibility and normalize_scores
#77
ghuls
closed
1 year ago
1
Reduce memory usage of impute_accessibility significantly.
#76
ghuls
closed
1 year ago
0
pycisTopic/Scenic+ human cerebellum single-cell multiome tutorial issue
#75
etiennedanis
closed
1 year ago
2
Bug report [BUG] read_csv() got an unexpected keyword argument 'sep'
#74
li-xuyang28
closed
1 year ago
2
Previous
Next