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alphafold

Open source code for AlphaFold.

alternative-splicing-study-under-mineral-nutrient-deficiency

anchorwave

sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

annotation_go.kegg.cog

整合型的对于生物学注释的信息/GO和KEGG全谱注释和富集

atlantic

Integrated analysis of genomes, transcriptomes, proteomes and drug responses of cancer cell lines (CCLs) is an emerging approach to uncover molecular mechanisms of drug action. We extend this paradigm to measuring proteome activity landscapes by acquiring and integrating quantitative data for 10,000 proteins and 55,000 phosphorylation sites (p-sites) from 125 CCLs. These data are used to contextualize proteins and p-sites and predict drug sensitivity. For example, we find that Progesterone Receptor (PGR) phosphorylation is associated with sensitivity to drugs modulating estrogen signaling such as Raloxifene. We also demonstrate that Adenylate kinase isoenzyme 1 (AK1) inactivates antimetabolites like Cytarabine. Consequently, high AK1 levels correlate with poor survival of Cytarabine-treated acute myeloid leukemia patients, qualifying AK1 as a patient stratification marker and possibly as a drug target. We provide an interactive web application termed ATLANTiC (http://atlantic.proteomics.wzw.tum.de), which enables the community to explore the thousands of novel functional associations generated by this work.

auto_martini

Automatic MARTINI parametrization of small organic molecules

bpforms

Toolkit for concretely describing non-canonical DNA, RNA, and proteins

cegma_v2

The final version 2 release of our software to detect core genes in eukaryotic genomes

chia-pet2

a versatile and flexible pipeline for analysing different variants of ChIA-PET data

cli

the package manager for JavaScript

cobind

collocation analysis of genomics regions

deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications

deepwas

DeepWAS: Directly integrating regulatory information into GWAS using machine learning

devilyuan

DevilYuan量化交易平台 可视化股票量化系统，支持选股，历史数据自动下载，策略回测及参数优化，实盘交易和常用的统计功能

edta

Extensive de-novo TE Annotator

fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data

ggcor

Extended tools for correlation analysis and visualization.

gomap-singularity

GOMAP-Singularity is the containerized version of GOMAP

hcasmceqtlviewer

HCASMCeQTLviewer is a combined bash/R/awk script to view eQTL box/dot plots for a specific gene/SNP cis and trans eQTL association in human coronary artery smooth muscle cells, one of the crucial cell types that are involved in atherosclerotic process of the blood vessel.

hicplotter

“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

hot_scan

hot_scan is a free software to detect genomic regions unusually rich (hotspot) in a given pattern via scan statistics

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

lcv

Software implementing the Latent Causal Variable Model

ldsc

LD Score Regression (LDSC)

manhattan-plot-eqtls-per-gene

mcsplicer

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

mwget

myscripts

Some useful scripts or awk program for dealing with gromacs data