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aertslab
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pycisTopic
pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
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No module named 'pycisTopic.gene_activity'
#191
Melody-cell
opened
1 day ago
1
If I get a low TSS enrichment, how can I filter it effectively?
#188
Melody-cell
closed
3 days ago
0
After add.cell_data to cisTopic_Object , it appears NaN
#187
Melody-cell
closed
3 days ago
8
Bug report [BUG] about tutorial
#186
Keep-Raining
opened
2 weeks ago
1
The data appears to lie in a lower-dimensional subspace of the space
#185
Melody-cell
opened
2 weeks ago
5
fail to run AUCell_direct due to memory.
#184
JinKyu-Cheong
opened
2 weeks ago
0
Add pycisTopic images to DockerHub
#182
massonix
opened
3 weeks ago
1
run_umap error
#181
sugiYag
closed
4 weeks ago
0
export_pseudobulk error
#180
sugiYag
closed
1 month ago
0
1Tb memory is insufficient for normalize_scores
#179
JinKyu-Cheong
opened
1 month ago
7
Memory speedup
#178
LisaMMilchsack
closed
1 month ago
0
[Tutorial] [246] export_gene_activity_to_loom important in SCENIC+ analyses?
#177
yojetsharma
opened
1 month ago
1
get a lower TSS enrichmet
#176
GGboy-Zzz
closed
1 month ago
5
Feature request [FEATURE] DARs plotting options: is there a way to generate coverage plots instead of UMAP plots?
#175
yojetsharma
opened
1 month ago
0
export_pseudobulk about question
#174
sugiYag
opened
1 month ago
0
Installation error
#173
juhi-ku
closed
1 month ago
1
'export_pseudobulk' output difference log
#172
GGboy-Zzz
opened
2 months ago
1
pandas.errors.InvalidIndexError: Reindexing only valid with uniquely valued Index objects
#171
Quentin-bioinfo
opened
2 months ago
4
plot_metadata: X11 connection rejected because of wrong authentication / Cannot load backend 'TkAgg' which requires the 'tk' interactive framework, as 'headless' is currently running
#170
strawberry098
opened
2 months ago
1
SCENIC+: pycistopic QC errors
#169
skoturan
opened
2 months ago
2
Bug report [BUG] cistopic_obj has nan values for sample and leiden column after adding cell_data
#168
yojetsharma
closed
1 month ago
5
Bug report [BUG] Trying to merge (cis_object_list) but gives an error that it is not defined
#167
yojetsharma
closed
1 month ago
6
create_cistopic_object_from_fragments ValueError
#166
Yiming-Huang-neuron
closed
2 months ago
0
Installation error
#165
ghost
opened
2 months ago
4
Error while running run_cgs_models_mallet()
#164
skoturan
closed
2 months ago
2
pycistopic qc error
#163
Yiming-Huang-neuron
closed
2 months ago
2
Bug report [Pycistopic Temporary Fragment file cannot be found]
#162
yrsong001
opened
2 months ago
2
cell_topic_heatmap color_dictionary can't be None
#161
camiel-m
closed
2 months ago
7
run_umap error
#160
strawberry098
opened
2 months ago
3
Feature request [FEATURE] Easily understandable tutorials
#159
yojetsharma
closed
1 month ago
0
bugfix read_fragments polars dynamic dtype
#158
camiel-m
closed
2 months ago
3
Bug report [compute_qc_stats update with v2 is no longer compatible with v1.01 workflow]
#157
ethanfenton
closed
2 months ago
3
find_highly_variable_features [PERFORMANCE]
#156
maithermbarros
opened
3 months ago
9
UnicodeDecodeError (QC step) [BUG]
#154
jklvrt
closed
3 months ago
1
RunTime error in Mallet returned non-zero exit status 134
#152
ashleighthomas
closed
3 months ago
1
Calling export_pseudobulk returns TypeError in function enable_string_cache() [BUG]
#151
ashleighthomas
closed
3 months ago
4
Guidance on topic model selection
#150
AmosFong1
closed
3 months ago
0
Polars 1xx
#149
ghuls
opened
4 months ago
0
Avoid making dense matrix in `create_cistopic_object_from_fragments` reduces memory 50X [PERFORMANCE]
#148
davidhbrann
opened
5 months ago
5
Cargo, the Rust package manager, is not installed or is not on PATH.
#147
massonix
opened
5 months ago
6
KeyError: 'cell' when running dimentionality reducition Bug report [BUG]
#144
degrainger
closed
6 months ago
2
pyGREAT gives error: AttributeError: 'NoneType' object has no attribute 'text
#143
MubasherMohammed
opened
6 months ago
2
Memory issue even after bigmem
#142
TingTingShao
opened
6 months ago
7
OpenBLAS warning
#141
TingTingShao
closed
6 months ago
3
models
#140
TingTingShao
closed
5 months ago
2
consensus_peaks.to_bed
#139
TingTingShao
closed
6 months ago
1
linux installaton problem Bug report [BUG]
#138
hshcao
closed
6 months ago
1
Error when running run_cgs_models_mallet
#137
EddieLv
closed
6 months ago
2
cannot import name 'triu' from 'scipy.linalg'
#135
kakaisi
closed
7 months ago
1
region_sets
#134
TingTingShao
closed
7 months ago
2
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