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adult_brain_somatic_mosaicism

This repository collects pipelines, codes, and some intermediate results for adult brain somatic mosaicism study.

atac-seq

awesome_spatial_omics

tools and notes for spatial omics

brca_cell_atlas

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".

chatgpt

Lightweight package for interacting with ChatGPT's API by OpenAI. Uses reverse engineered official API.

cnaviz

comparative-annotation-toolkit

doubletfinder

R package for detecting doublets in single-cell RNA sequencing data

fastgithub

github加速神器，解决github打不开、用户头像无法加载、releases无法上传下载、git-clone、git-pull、git-push失败等问题

ffq

A tool to find sequencing data and metadata from public databases.

genetrajectory

R implementation of GeneTrajectory

genomesearch

Quickly search for closely related microbial genomes using a marker-gene based approach.

genovi

GenoVi, an automated customizable circular genome visualizer for bacteria and archaea

gget

🧬 gget enables efficient querying of genomic reference databases

gptcelltype

gseapy

Gene Set Enrichment Analysis in Python

guideline-for-computational-biology-and-bioinformatics

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

igv_utils

utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.

kallisto

Near-optimal RNA-Seq quantification

kraken2_classification

Snakemake workflow for metagenomic classification with Kraken2

lapa

Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.

ldsc

LD Score Regression (LDSC)

long-read-pipelines

Long read production pipelines

metabinner

multi-omics-cancer-benchmark

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

multivelo

Multi-omic velocity inference

mutationtimer

An R package to time somatic mutations

ncem

Learning cell communication from spatial graphs of cells