a-slide / pycoMeth

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

a-slide/pycoMeth Issues

Reduce memory footprint for large datasets
Closed 3 years ago3
Improve methylation scoring method
Closed 3 years ago
Improve differential methylation statistical test
Closed 3 years ago
Add support for Megalodon and DeepSignal
Closed 3 years ago4
[Question] For proper usage on differential methylation
Closed 3 years ago2
Is it possible to use `Comp_Report` without a gff3 file?
Closed 3 years ago1
Add Volcano like plot
Closed 3 years ago
Invalid Input file type
Closed 3 years ago7
Insufficient effect size / samples
Closed 3 years ago3
Missing submodule CpG_Aggregate
Closed 3 years ago2
pycoMeth Nextflow pipeline
Closed 3 years ago2
No valid sites left after coverage filtering
Closed 4 years ago2
pycoMeth.common.pycoMethError: Invalid input file type passed (nanopolish_fn). Expecting Nanopolish call_methylation output TSV file
Closed 4 years ago7
Comp_report exiting with invalid file input type from Interval_Aggregate
Closed 4 years ago1
ZeroDivisionError: float division by zero when running `Meth_Comp`
Closed 4 years ago3
Use two-sided alternative in mannwhitneyu test
Closed 4 years ago1
transcript id, gene id and transcript name in interval report
Closed 4 years ago
`ERROR: Not all the chromosomes found in the data file are present in the GFF3 file.` but this is incorrect
Closed 4 years ago3
Not recognising nanopolish file
Closed 4 years ago5
What CpG modification is support in pycoMeth
Closed 4 years ago1
Write a dedicated Snakemake workflow
Closed 4 years ago2
Option to generate a heatmap per individual for Interval comparison
Closed 5 years ago1
Documentation of output files
Closed 5 years ago3
division by zero in CGI_Finder
Closed 5 years ago2
ValueError: Precision not allowed in integer format specifier
Closed 5 years ago13