Starlitnightly / omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

https://starlitnightly.github.io/omicverse/

Starlitnightly/omicverse Issues

Data lost with STAGATE_pyG
Closed a month ago2
Added `CytoTrace2` to calculate the developmental potential
Closed a month ago
Request for TCGA analysis
Updated a month ago2
presence of down regulated genes in the pathway analysis with AUCell
Updated a month ago3
Error pathway enrichment figure by using ov.bulk.geneset_plot
Updated a month ago1
bug in survial_init
Updated a month ago1
Issue Regarding Survival Analysis
Updated a month ago2
Conflict on scanpy and omicverse
Updated a month ago2
Installation Win
Updated a month ago4
Request for bulk count to CPM/TPM/FPKM function
Updated a month ago1
H should have the same dtype as X. Got H.dtype = float32.
Updated a month ago3
When using bulk2single, should the bulk data use counts, tpm, deseq_normalize, or other types of data?
Updated a month ago3
anndata_to_CPU() got an unexpected keyword argument 'layers'
Closed a month ago2
ov.pp.qc() Error
Closed 2 months ago2
module 'omicverse.pl' has no attribute 'contour'
Closed 2 months ago1
Error for ov.utils.cal_paga and ov.single.pyVIA
Closed 2 months ago6
Added argument descriptions to all functions in the single directory
Closed 2 months ago
Added argument description of space function
Closed 2 months ago1
Added `plot_spatial` like cell2location
Closed 2 months ago
Added package PROST to calculate spatial variable gene
Closed 2 months ago
Added GPTCelltype
Closed 2 months ago
pip installation error
Closed 2 months ago
Gene set enrichment analysis error : Exception: No gene sets passed through filtering condition
Closed 3 months ago
A problem about batch correction in single-cell-tutorial's code
Closed 3 months ago4
Encounter Error When Installing OmicVerse on Ubuntu 22.04 [Preparing metadata (setup.py) ... error]
Closed 3 months ago12
Error in enrich_res=gsea_obj.enrichment()
Closed 3 months ago2
DEG plot_volcano KeyError: 'explode'
Closed 3 months ago4
defined order for the plot of groups
Closed 3 months ago1
Bulk Analysis about DiffAnalysis using Omicverse
Closed 3 months ago3
implement other GPU based package to handel large scale cells (>1 million)
Closed 3 months ago1
LibMambaUnsatisfiableError when installing omicverse on win-64
Closed 3 months ago2
Installation Recommendation for people using Conda or pip
Updated 3 months ago2
Sample (dataset) question in the tutorial
Closed 3 months ago2
Encounter Error When Installing OmicVerse on Debian10.7.0
Closed 3 months ago
LibMambaUnsatisfiableError: Encountered problems while solving
Closed 3 months ago2
Where is the function ov.pl.cellproportion?
Closed 3 months ago2
Error on Python 3.12: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?
Closed 3 months ago1
KeyError: 'None is not a known colormap name'
Closed 3 months ago1
Could not show the pictures after run the code "ov.utils.embedding" in WSL2
Closed 3 months ago1
Some errors when i pip this package
Closed 3 months ago2
More complete gene ensembl id -> hgnc symbol pairs table
Updated 4 months ago1
How to get the filtered dataframe with dds.foldchange_set?
Closed 6 months ago2
To do list in the version of `1.5.2`
Closed 6 months ago
Some suggestions about OV
Updated 7 months ago8
A question about the existence of randomness in OV computed metacells
Closed 7 months ago6
Actually,not retain only the highest expressed gene
Updated 7 months ago1
A problem about the TCGA survival analysis
Updated 7 months ago1
scikit-learn module conflicts
Closed 7 months ago1
Inquiry about Preprocessing with Specific Gene Exclusion Based on "Liver tumour immune microenvironment subtypes and neutrophil heterogeneity" Study
Updated 7 months ago1
Exponential Increase in Data Size After Single-cell Data Processing with OV
Closed 8 months ago1