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Starlitnightly
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omicverse
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
https://starlitnightly.github.io/omicverse/
GNU General Public License v3.0
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Add guidance on using local LLMs for cell types annotation
#99
fredsamhaak
closed
4 days ago
1
Data lost with STAGATE_pyG
#98
liuxiawei
closed
4 days ago
2
Added `CytoTrace2` to calculate the developmental potential
#97
Starlitnightly
closed
6 days ago
0
Add a function of cell types annotation with local LLMs
#96
fredsamhaak
closed
5 days ago
5
Request for TCGA analysis
#95
Jonyyqn
opened
1 week ago
2
When using bulk2single, should the bulk data use counts, tpm, deseq_normalize, or other types of data?
#94
Hennery02
opened
1 week ago
3
anndata_to_CPU() got an unexpected keyword argument 'layers'
#93
xuzhougeng
closed
2 weeks ago
2
Revise normalize_bulk function #83
#92
JuliaMYQ
closed
3 weeks ago
0
add arguments descriptions for single #84
#91
JuliaMYQ
closed
3 weeks ago
0
Update the annotation of space-related function.
#90
DBinary
closed
3 weeks ago
0
Added `plot_spatial` like cell2location
#89
Starlitnightly
closed
3 weeks ago
0
Added package PROST to calculate spatial variable gene
#88
Starlitnightly
closed
3 weeks ago
0
add descriptions and normalize_bulk function #83
#87
JuliaMYQ
closed
3 weeks ago
1
Error for ov.utils.cal_paga and ov.single.pyVIA
#86
looppy95
closed
3 weeks ago
6
H should have the same dtype as X. Got H.dtype = float32.
#85
christophechu
opened
1 month ago
3
Added argument descriptions to all functions in the single directory
#84
Starlitnightly
closed
3 weeks ago
0
Request for bulk count to CPM/TPM/FPKM function
#83
erwusht
opened
1 month ago
1
Added GPTCelltype
#82
Starlitnightly
closed
1 month ago
0
Added argument description of space function
#81
Starlitnightly
closed
3 weeks ago
1
module 'omicverse.pl' has no attribute 'contour'
#80
christophechu
closed
3 weeks ago
1
pip installation error
#79
panyiling
closed
1 month ago
0
Update the function of ov.pl.embedding()
#78
DBinary
closed
1 month ago
0
ov.pp.qc() Error
#77
czy1238677
closed
3 weeks ago
2
Gene set enrichment analysis error : Exception: No gene sets passed through filtering condition
#76
asd519627326
closed
1 month ago
0
Installation Win
#75
RubyLiu206
opened
1 month ago
4
Conflict on scanpy and omicverse
#74
yifanfu01
opened
1 month ago
2
LibMambaUnsatisfiableError when installing omicverse on win-64
#73
kakkboy
closed
1 month ago
2
Sample (dataset) question in the tutorial
#72
asd519627326
closed
1 month ago
2
Encounter Error When Installing OmicVerse on Debian10.7.0
#71
asd519627326
closed
2 months ago
0
LibMambaUnsatisfiableError: Encountered problems while solving
#70
pickingastar
closed
2 months ago
2
KeyError: 'None is not a known colormap name'
#69
Donbbit
closed
2 months ago
1
Issue Regarding Survival Analysis
#68
xianjieshen
opened
3 months ago
2
Error on Python 3.12: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?
#67
sq-shuqian
closed
2 months ago
1
More complete gene ensembl id -> hgnc symbol pairs table
#66
ElderMedic
opened
3 months ago
1
Encounter Error When Installing OmicVerse on Ubuntu 22.04 [Preparing metadata (setup.py) ... error]
#65
michael-yuyuan
closed
1 month ago
12
Where is the function ov.pl.cellproportion?
#64
christophechu
closed
2 months ago
2
update the function of spaceflow
#63
DBinary
closed
4 months ago
0
bug in survial_init
#62
aopisco
opened
4 months ago
1
update the fcuntion and tutorials of plotting
#61
DBinary
closed
5 months ago
0
Installation Recommendation for people using Conda or pip
#60
mugpeng
opened
5 months ago
2
Error in enrich_res=gsea_obj.enrichment()
#59
erwusht
closed
1 month ago
2
How to get the filtered dataframe with dds.foldchange_set?
#58
erwusht
closed
5 months ago
2
Fix the simba error 2ed
#57
mugpeng
closed
5 months ago
0
Fix the error
#56
mugpeng
closed
5 months ago
0
Error pathway enrichment figure by using ov.bulk.geneset_plot
#55
wanglifangelena
opened
5 months ago
1
A problem about batch correction in single-cell-tutorial's code
#54
DestinyXuanQAQ
closed
1 month ago
4
DEG plot_volcano KeyError: 'explode'
#53
wanglifangelena
closed
1 month ago
4
Update the function and tutorial of ov.bulk.geneset_plot.
#52
DBinary
closed
5 months ago
0
Could not show the pictures after run the code "ov.utils.embedding" in WSL2
#51
DestinyXuanQAQ
closed
2 months ago
1
update the tutorial of STAligner
#50
DBinary
closed
5 months ago
0
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