Additional code and analysis from the single-cell integration benchmarking project

Render markdown on the CLI, with pizzazz! 💅🏻

微舆：人人可用的多Agent舆情分析助手，打破信息茧房，还原舆情原貌，预测未来走向，辅助决策！从0实现，不依赖任何框架。

Code for the analyses in the paper "A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity"

Single cell atlas of the hearts of patients with dilated cardiomyopathy

Single-cell Colorectal Cancer Atlas with 4.27M cells

A single cell transcriptome atlas of the developing zebrafish hindbrain.

Pan-cancer human brain metastases atlas at single-cell resolution

Pipeline framework for iteratively and reproducibly building and evaluating single cell atlases

Single-cell RNA-seq analysis from "Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord" (2019)

Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs

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

Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)

A code repository for the analyses conducted in the paper titled "Uncovering the multivariate genetic architecture of frailty with genomic structural equation modelling" by Foote et al. (2025)

Nextflow pipeline for GWAS analysis of pangenome variants (SNP, INDEL, SV)

This script contains the scripts used to detect SVs in a population using a graph-based pangenome and short reads, run GWAS with GLM and BLINK methods, and perform genomic prediction.

In this repository, you can find the datasets, scripts, and plots used in my Bachelor’s thesis “Fine-Scale Recombination Maps of The Cattle Genome Inferred by Linkage Disequilibrium”.

Scripts and data for red drum linkage map manuscript

set of scripts to generate linkage map with LepMap3

We built a linkage map of Mimulus using the software OneMap.

Linkage map files for maize weevil

Constructing a high density linkage map and QTL analysis

A collection of WDL bioinformatic workflows to benchmark markers coming from different pipelines using linkage map quality as a diagnosis.

A software tool that builds genetic linkage maps efficiently and accurately

Pipeline for linkage map construction from NGS data

A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.