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Kiran N' Bishwa's Projects

ase-cadg icon ase-cadg

Pipeline for ASE (allele specific expression) using competitive alignment to diploid genome

classifier-reborn icon classifier-reborn

A general classifier module to allow Bayesian and other types of classifications. A fork of cardmagic/classifier.

cyvcf2 icon cyvcf2

cython + htslib == fast VCF and BCF processing

emase icon emase

Expectation-Maximization algorithm for Allele-Specific Expression

g2gtools icon g2gtools

Custom genome creation and coordinate conversion

hipstr-tutorial icon hipstr-tutorial

Simple tutorial demonstrating how to run HipSTR with human WGS data

phase-extender icon phase-extender

A python program that uses ReadBack phased haplotypes in population of samples and returns extended haplotype blocks.

phase-imputer icon phase-imputer

Phase imputation in RBphased haplotypes using first order markov chains.

phase-stitcher icon phase-stitcher

a python program to stitch the ReadBack phased haplotypes in F1 hybrids.

phaseit icon phaseit

A pipeline for phasing haploptypes using short readbackphased haplotype blocks in population of samples.

phaser icon phaser

phasing and Allele Specific Expression from RNA-seq

phaserb icon phaserb

A tool for running readbackphasing on VCF using BAM (reference genome aligned genome or RNAseq reads).

plotawesome icon plotawesome

This repo contains collections of plots and codes used to generate it.

pyvcf icon pyvcf

A Variant Call Format reader for Python.

seqnature icon seqnature

Seqnature: incorporate SNPs and Indels into a reference genome

smalltools icon smalltools

Collection of several small tools. These tools stay here temporarily and may move to other major repositories as they evolve.

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