Pinned Repositories
annovarR
The annovarR package provides R functions as well as database resources which offer an integrated framework to annotate genetic variants from genome and transcriptome data.
bio304-book
Bookdown based course notes for Bio 304 at Duke University, taught by Paul Magwene
bioinformatics123
bioweb
DeMix
hypeR
An R Package for Geneset Enrichment Workflows
manuscripts
Code and data for manuscripts.
MMR
C. elegans and ICGC cancer data analysis for (Meier, Volkova et al. 2017)[https://www.biorxiv.org/content/biorxiv/early/2017/06/13/149153.full.pdf].
monocle2-rge-paper
Scripts needed to generate the figures for the Monocle 2 paper (Qiu et al, 2017)
the-craft-of-selfteaching
One has no future if one couldn't teach themself.
xchromosome219's Repositories
xchromosome219/hypeR
An R Package for Geneset Enrichment Workflows
xchromosome219/the-craft-of-selfteaching
One has no future if one couldn't teach themself.
xchromosome219/simplifyEnrichment
Simplify functional enrichment results
xchromosome219/bamQC
Workflow to run bam-qc-metrics (https://github.com/oicr-gsi/bam-qc-metrics)
xchromosome219/BarrettsProgressionRisk
An R package to process and predict risk of adenocarcinoma progression from shallow whole-genome sequencing data.
xchromosome219/battenberg
Battenberg R package for subclonal copynumber estimation
xchromosome219/create_cisTarget_databases
Create cisTarget databases
xchromosome219/E-MTAB-6141
Data from Lewis, Barnes, Blighe et al., Cell Rep. 2019 Aug 27; 28(9): 2455–2470.e5.
xchromosome219/FriendsDontLetFriends
Friends don't let friends make certain types of data visualization - What are they and why are they bad.
xchromosome219/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。
xchromosome219/immunedeconv
A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter)
xchromosome219/Ini-seq-2
Ini-seq 2 origin caller
xchromosome219/lncRNAs
script of lncRNA project
xchromosome219/MOVICS
Multi-Omics integration and VIsualization in Cancer Subtyping
xchromosome219/neoantigen-vaccine-pipeline
Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines
xchromosome219/neoantigens
🏺 Exploring novel tumor epitope identification
xchromosome219/nichenetr
NicheNet: predict active ligand-target links between interacting cells
xchromosome219/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.
xchromosome219/plyranges
A grammar of genomic data transformation
xchromosome219/presentations
NIH BYOB Presentation Materials
xchromosome219/Python-100-Days
Python - 100天从新手到大师
xchromosome219/scclusteval
Single Cell Cluster Evaluation
xchromosome219/SCENICprotocol
A scalable SCENIC workflow for single-cell gene regulatory network analysis
xchromosome219/single-cell-pseudotime
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
xchromosome219/Single-cell-regulatory-network
xchromosome219/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"
xchromosome219/SingleCellWorkshop
xchromosome219/SparK
Publication quality NGS track plotting
xchromosome219/spectrum-tme
Supporting material for publication: "Ovarian cancer mutational processes drive site-specific immune evasion"
xchromosome219/ulcerative_colitis