xchromosome219

hypeR

An R Package for Geneset Enrichment Workflows

the-craft-of-selfteaching

One has no future if one couldn't teach themself.

simplifyEnrichment

Simplify functional enrichment results

bamQC

Workflow to run bam-qc-metrics (https://github.com/oicr-gsi/bam-qc-metrics)

BarrettsProgressionRisk

An R package to process and predict risk of adenocarcinoma progression from shallow whole-genome sequencing data.

battenberg

Battenberg R package for subclonal copynumber estimation

create_cisTarget_databases

Create cisTarget databases

E-MTAB-6141

Data from Lewis, Barnes, Blighe et al., Cell Rep. 2019 Aug 27; 28(9): 2455–2470.e5.

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

gpt_academic

为GPT/GLM提供图形交互界面，特别优化论文阅读润色体验，模块化设计支持自定义快捷按钮&函数插件，支持代码块表格显示，Tex公式双显示，支持Python和C++等项目剖析&自译解功能，PDF/LaTex论文翻译&总结功能，支持并行问询多种LLM模型，支持清华chatglm等本地模型。兼容复旦MOSS, llama, rwkv, 盘古等。

immunedeconv

A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter)

Ini-seq-2

Ini-seq 2 origin caller

lncRNAs

script of lncRNA project

MOVICS

Multi-Omics integration and VIsualization in Cancer Subtyping

neoantigen-vaccine-pipeline

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

neoantigens

🏺 Exploring novel tumor epitope identification

nichenetr

NicheNet: predict active ligand-target links between interacting cells

OK-Seq

R package for the analysis of OK-Seq data to study DNA replication fork directionality: from count matrices, RFD calculation to inititation/termination zone calling.

plyranges

A grammar of genomic data transformation

presentations

NIH BYOB Presentation Materials

Python-100-Days

Python - 100天从新手到大师

scclusteval

Single Cell Cluster Evaluation

SCENICprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis

single-cell-pseudotime

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

Single-cell-regulatory-network

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

SingleCellWorkshop

SparK

Publication quality NGS track plotting

spectrum-tme

Supporting material for publication: "Ovarian cancer mutational processes drive site-specific immune evasion"

ulcerative_colitis