Akhilesh Kaushal's repositories
TCGA2BED
The Cancer Genome Atlas Data Extraction and Conversion Tool
GEA_Community_Detection
Overrepresentation analysis for KEGG and PID pathways using community detection
r-shiny-mysql-template
This example shows how to use Anychart library with the R programming language, Shiny web framework and MySQL database.
quip
Compressing next-generation sequencing data with extreme prejudice.
ARGON
Fast, whole-genome simulation of the discrete time Wright-Fisher process
mint
A pipeline for the integration of DNA methylation and hydroxymethylation data
ngsplot
Quick mining and visualization of NGS data by integrating genomic databases
coda
Coda: a convolutional denoising algorithm for genome-wide ChIP-seq data
continuous_analysis
Computational reproducibility using Continuous Integration to produce verifiable end-to-end runs of scientific analysis.
ngseasy
Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
bioconductor-scraper
A scraper which tries to generate conda recipes for bioconductor and other needed R packages.
shinyproxy-LBI
docker image and Dockerfile build folder for LBI shinyproxy test
PRAD-compartments
Analysis scripts to accompany Simmons et al 2016 manuscript 'Integrating chromatin compartment maps with genome-wide transcription factor binding profiles and gene expression data identifies transcriptional drivers of prostate carcinogenesis'
pancancer-1
Pancancer related code and aux. data.
eQTL
eQTL analysis pipeline
chirpseq-analysis
converts chirpseq fastq files into bedgraphs suitable for downstream processing
continuous_analysis_rnaseq
Example of how continuous analysis can be used for RNA-Seq differential expression.
bayesianprobabilitiesworkshop
A collection of questions and solutions to problems presented at Rasmus Bååth's Bayesian probabilities workshop.
gbm_immune_validation
Validating glioblastoma immune cell immunohistochemsitry using computational deconvolution of TCGA tumors
nf1_inactivation
Using Machine Learning to Identify Glioblastoma patients with NF1 inactivation
ganalyse
Easy Analysis of RNASeq DE
Modular-Programming-with-Python
Modular-Programming-with-Python Code
LEM
A pipeline to extract leading edge metagene from GSEA results
TeachingMaterial
RNA-seq data analysis practical
GWAS-OLS-GLS
A few functions that perform GWAS using OLS and GLS