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2clike_analysis

Some of the mapping and normalization scripts used in our NCB paper PMID:31209294

batch-effect-removal-benchmarking

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

bhattacherjee_elal_nc_2019_somecode

Some Rmarkdown of the analysis Bhattacherjee et al, 2019. Contains some extra analysis and results not included

biallelic_hr

Source code and data for "Pan-cancer analysis of bi-allelic alterations in homologous recombination (HR) DNA repair genes" ; See manuscript @

bioinformatics-servers

收集生物专业科研数据分析中使用的在线生物信息学分析服务，按分子类型(DNA、RNA、Protein)和分析领域进行整理和分类！

biscuit_snakemake_workflow

Snakemake Workflow For WGBS Data

bms038_analysis

Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for manuscript https://doi.org/10.1016/j.cell.2017.09.028 See also http://www.ioexplorer.org for interactive visuallization

bulkseq

cardiac-progenitors

Single cell RNA-seq and ATAC seq analysis of cardiac progenitor cell transition states and lineage settlement

chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

chippipes

Pipelines for ChIP-seq / CUT&RUN / CUT&Tag etc. analysis

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline

chromhmm

cloops

Accurate and flexible loops calling tool for 3D genomic data based on un-supervised clustering and permuted local background.

complex_figure_examples

Gallery and R code for published scientific figures

crc_scrnaseq

figr

Functional Inference of Gene Regulation

gtex-single-nucleus-reference

Code repository for the snRNA-seq cross-tissue atlas project

hdwgcna_paper

Code used to run the data analysis in the hdWGCNA manuscript (Morabito et al 2022)

hic3dviewer

an interactive webbased tool for the interactive 3D visualization and exploratory analysis of Hi-C data.

hicexplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

https-github.com-shenorrlab-cellalign

jogiles_atac

liribo-seq

llm-scientific-feedback

Can large language models provide useful feedback on research papers? A large-scale empirical analysis.

pancanmet_analysis

Software and analysis of metabolism studies across multiple cancer types

plot1cell

rnaseq_snakemake

rnaseq_workflow

snakemake workflow for bulk RNA-seq workflow using STAR-edgeR