icbi-lab / infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

https://infercnvpy.readthedocs.io/en/latest/

icbi-lab/infercnvpy Issues

infercnvpy.tl.infercnv result matrix is of incorrect dimensionality
Closed 4 months ago2
stable release
Updated 6 months ago1
Accessing Metadata from AnnData
Updated 8 months ago6
genomic_position_from_gtf Attribute Error
Closed 9 months ago3
TypeError: read_csv() got an unexpected keyword argument 'sep' in infercnvpy.io.genomic_position_from_gtf
Closed 9 months ago7
rename toggle_string_cache to enable_string_cache
Closed 9 months ago3
Limit color scale heat map
Closed 9 months ago3
infercnvpy.pl.chromosome_heatmap doesn't pass dendrogram data to scanpy.pl.heatmap
Closed 9 months ago3
NA/NaN/Inf in foreign function call (arg 10)
Closed 9 months ago1
copykat py2rpy error
Closed 9 months ago2
Identifying spike-in cells using InferCNVpy
Closed 9 months ago4
Use statistical tests to improve CNV calling
Closed 9 months ago
cnv.tl.infercnv error
Closed 9 months ago3
The tutorial may need to be updated
Closed 9 months ago
copykat with mouse data
Closed a year ago8
Are we able to use output of infercnvpy for drawing phylogenetic trees?
Updated a year ago1
need at least one array to concatenate when doing cnv.tl.infercnv()
Closed 2 years ago12
Citation
Updated a year ago4
infercnvpy.pl.chromosome_heatmap shows 1e9 map values for copykat results
Updated a year ago4
inferCNV output matrix has the same dimension with different window size
Closed a year ago2
Inconsistent use_rep usage through src files
Closed a year ago2
copycat memory issue
Closed a year ago2
how are gene counts in groups that are all 0 handled
Updated a year ago
heatmap function is not recognising dendogram
Closed a year ago2
genomic_position_from_gtf
Closed a year ago2
Shape of the output of cnv.tl.infercnv
Closed 2 years ago1
How to adjust the scale bar of chromosome_heatmap
Closed 2 years ago6
Ith score
Closed 2 years ago4
CopyKAT - got an unexpected keyword argument 'norm_cell_names'
Closed 2 years ago2
Using reference datasets
Updated 2 years ago1
Make nextflow pipeline to run copyKAT and SCEVAN
Updated 2 years ago2
Add a tool for ITHCNA
Closed 2 years ago2
add SCEVAN
Closed 2 years ago1
Add copykat to tutorial
Closed 2 years ago5
Add to Bioconda
Closed 3 years ago1
Add wrapper for copyKAT
Closed 3 years ago2
Pre-processing data?
Closed 3 years ago2
summary bug
Closed 3 years ago2
Heatmap chrom lenght - col width
Updated 3 years ago1
considering numerically order the chromosome label `chr_pos` on the `chromosome_heatmap` function?
Closed 3 years ago9
provided out is the wrong size for the reduction
Closed 3 years ago1
ValueError: need at least one array to concatenate
Updated 3 years ago11
Function to classify malignant/non-malignant cells
Updated 3 years ago2
Scanpy 10x Implementation
Closed 3 years ago4
What are the units of 'window_size'?
Closed 3 years ago2
ValueError: need at least one array to concatenate
Closed 3 years ago1
HMM-based CNV caller
Updated 3 years ago