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alphafold

Open source code for AlphaFold.

asymptomatic_transmission_covid

betacat

Code for computational RNASeq, scRNASeq and ATACSeq analysis used in the manuscript "Differential regulation of β-catenin-mediated transcription governs identity of murine intestinal epithelial stem cells"

bsmn-pipeline

BSMN common data processing pipeline

celltalker

Inference of cell-cell communication from single-cell RNAseq data

clingen-fvg

Scripts used in bioinformatics analysis for the Clingen-FVG project

convergent_rbd_evolution

covid-19_map

cpi1000_paper

cutprimers

curPrimers is a tool for trimming primer sequences from amplicon based NGS reads

degs-repo

dna-binding-protien-prediction

this project mainly aims to predict the DNA binding proteins from the given fasta format then it will connect to the UniProt database and print its functions

dragonsc

Deterministic annealing gaussian mixtures models for single cell RNAseq

ecgea

egea

Every Gene Ever Annotated in published GWAS

enrichment-analysis

From RNA-seq raw reads to enriched pathways by DEGs

eosinophils_scrnaseq

epigraphdb-pqtl

This is the github repository to provide the R scripts been used in the phenome-wide Mendelian randomization study of plasma proteome.

galeano-nino-bullman-intratumoral-microbiota_2022

Analysis code used in Galeano Nino et al., Impact of Intratumoral Microbiota on Spatial and Cellular Heterogeneity in human cancer. 2022

geoquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

gistic2

Genomic Identification of Significant Targets in Cancer (GISTIC), version 2

gistic2_example

a example script and reference files to run GISTIC2

hyeon_et_al_pdac_nature_cancer

infercnv

Inferring CNV from Single-Cell RNA-Seq

influenzafitnessinference

Supplementary code and data accompanying the manuscript titled "Inferring the intrinsic mutational fitness landscape of influenza-like evolving antigens from temporally ordered sequence data"

insaflu

INSaFLU (“INSide the FLU”) is an influenza-oriented bioinformatics free web-based suite

iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

kedmi-citeseq

Code for the Kedmi et al paper

lasso_positions_sampling

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.