alaminzju

opendatatoronto

Access data from the City of Toronto Open Data Portal in R.

ASBanalyzer

A pipeline for analyzing allele specific binding sites.

PathTurbEr

Pathway Perturbation Driver identification

SmartGPT

A nodejs implementation of AI Explained on youtube's SmartGPT prompting strategy for getting better responses from gpt4.

CellRegMap_analyses

Repository containing the code to reproduce the analyses described in the CellRegMap manuscript

onek1k_phase1

Contains code to analyze the OneK1K data and perform eQTL mapping of 14 cell types

scONE-seq-data-processing

scONE-seq analysis codes

chatgpt

Interface to ChatGPT from R

askgpt

A chat interface build on top of OpenAI's API endpoints

RTutor

Chat with your data via AI. https://RTutor.ai

lattice

Trellis Graphics for R

BLMRM

A R package to perform genome-wide allele-specific expression

WASP

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery

allele-specific-expression

Pipeline to perform the allele-specific expression analysis (based on the work by Skelly et al. 2011)

atom

:atom: The hackable text editor

scPolyA-seq

https://pubmed.ncbi.nlm.nih.gov/36454750/

sickle

Windowed Adaptive Trimming for fastq files using quality

TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

vcfView

An interactive Rshiny tool designed to support the evaluation of somatic mutation calls from cancer sequencing data. The tool takes as input a single variant call format (VCF) file and enables researchers to explore the impacts of analytical choices on the mutant allele frequency spectrum, on mutational signatures and on annotated somatic variants in genes of interest. It allows variants that have failed caller filters to be re-examined in order to improve sensitivity or guide strategies for optimal sample / sequencing preparation. It is extensible allowing other algorithms to take advantage of its VCF preprocessing capabilities.

STAR

RNA-seq aligner

cgpVAF

Calculates the Variant Allele Fraction of variants in VCF files

allelecounter

Counts the number of reads which map to either the reference or alternate allele at each heterozygous SNP.

Qllelic

Enabling differential allele-specific analysis

ASEReadCounter_star

Preprocessing sequencing data for allele-specific analysis

eagle

An R package for detecting Gene-by-Environment (GxE) interaction effects on the transcriptome using Allele Specific Expression quantified from RNA-seq

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

Reinius_et_al_Nature_Genetics_2016

Repository code used for allele-specific gene expression analyses using single-cell RNA-seq data in Reinius/Mold et al. Nature Genetics 2016

scphaser

R package for haplotype phasing using single-cell RNA-seq data

vcftoolz

Tools for working with Variant Call Format files.

scAllele