13 projects
kreview
Evaluate cfDNA fragmentomics features for ctDNA detection
krewlyzer
Feature extraction tools for circulating tumor DNA from GRCh37 aligned BAM files
gbcms
Python implementation of GetBaseCountsMultiSample (gbcms) for calculating base counts in BAM files
py-gbcms
Deprecated: py-gbcms has been renamed to gbcms. Install gbcms instead.
genotype-variants
A tool for genotyping SNV, INDEL, and SV variants in genomic data.
fragscan_ct
This Python package, is designed to calculate the fragment length ratios from a BAM file using the input BED and reference genome files. The script provides several options for manipulating the input intervals and applying GC content correction to the coverage analysis.
postprocessing_variant_calls
This hosts multiple scripts necessary for filtering and processing of variant calls in the vcfs/txt file generated by callers.
biometrics
Package to generate sample based biometrics.
bed-lookup
Lookup a gene by coordinate from a bed
python-bed-lookup
multiqc-msk
Create aggregate bioinformatics analysis reports across many samples and tools
fgbio-postprocessing
fgbio_postprocessing
merge-fastq
Package to merge multiple pair of pair-end fastq data
