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agilent

Microarray analysis of agilent data

aips

Absolute Inference of Patient Signatures

alternative-splicing-tools

A list of alternative splicing analysis resources

aneuploidy_score

R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al. (https://doi.org/10.1038/s41467-020-14286-0)

annopeak

annovar2maf

Tiny python script to generate MAF files from output generated by standard annotation programs

apasurvey

A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data

aplot

decorate a plot with associated information

atac-seq

Basic workflow for ATAC-seq analysis

atacseq

ATAC-seq peak-calling, QC and differential analysis pipeline

atacseq-1

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

awesome

Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.

awesome-expression-browser

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

awesome_spatial_omics

tools and notes for spatial omics

batch-effect-removal-benchmarking

A benchmark of batch-effect correction methods for single-cell RNA sequencing data

batcheffectspackage

The MBatch R package and Docker image are designed to help assess and correct for batch effects.

beadanalyze

Automated differential expression analysis for Illumina beadarrays (HT12 V4 arrays).

biomethyl

An R package to interpret biological trends from DNA methylation data

brca-lrseq-pipeline

Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.

calculating-fusion-twas-weights-pipeline

This is a pipeline for calculating weights for TWAS

cancer_notes

A continually expanding collection of cancer genomics notes and data

case_splicing

castin

CASTIN: CAncer-STromal INteractome analysis

catharanthus_scrna_seq

R scripts for bioRxiv submission

cb_sniffer

mutation(barcode) caller for 10x single cell data

cdseq_r_package

CDSeq R Package

cfdna

cheatsheet

Repository for the cheatsheet and R code for generating the examples displayed.

checkoverlap

An R package using Rcpp to check if SNPs in DNA segments or if DNA segments contain SNPs

chernobylthyroidcancer-methylation