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awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

bap

Bead-based single-cell atac processing

basevar

This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially for NIPT data

bayesr

Bayesian hierarchical model for complex trait analysis

cellranger

10x Genomics Single Cell Analysis

chromap

Fast alignment and preprocessing of chromatin profiles

cmplot

📊 Circular and Rectangular Manhattan Plot

cropgbm

dnbc4tools

DNBelab C Series single-cell RNA softare

dnbelab_c_series_ht_scrna-analysis-software

An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets

doubletfinder

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

dsb_manuscript

Code to reproduce results from manuscript "Normalizing and denoising protein expression data from droplet-based single cell profiling"

dynbenchmark

Comparison of methods for trajectory inference on single-cell data 🥇

episcanpy

Episcanpy: Epigenomics Single Cell Analysis in Python

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

gemma

Genome-wide Efficient Mixed Model Association

gensel

Anything related to GenSel program from Iowa State

gggenes

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

ggthemr

Themes for ggplot2.

ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees

intror

这是一本中文 R 语言入门书，基于最新 tidyverse 包。

kaml

:bicyclist: Kinship Adjusted Multi-Loci Best Linear Unbiased Prediction

lme4qtl

Mixed models @lme4 + custom covariances + parameter constraints

maestro

Single-cell Transcriptome and Regulome Analysis Pipeline

metaminimac2

metbrewer

Color palette package in R inspired by works at the Metropolitan Museum of Art in New York

microbe-seq

Single-cell genomic sequencing of the human gut microbiome

mmod

Differentiation statistics in R

netview

Mutual nearest neighbor graphs and data visualization for genomic population networks :octopus:

netviewp

NetView for Python