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pipeline-for-isoseq

pipelines

Analytical tools and pipelines for bulk and single cell epigenomic and human genetic data

plot1cell

python-data-visualization

Data visualization with Python

r-data-visualization

Data visualization with R

rna-seq-analysis

RNAseq analysis notes from Tommy Tang

rnaseq_ref_pipe

Run RNASeq analysis with reference genome based on the Tophat-Cufflinks pipeline.

scatac-pro

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

scdva

An R shiny based tool used for single cell RNA-seq data visualization and analysis.

scell_lung_adenocarcinoma

This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset

scrna-seq_notes

A list of scRNA-seq analysis tools

scrna.seq.course

Analysis of single cell RNA-seq data course

scvelo

RNA Velocity generalized through dynamical modeling

scwgcna

scWGCNA

seurat

R toolkit for single cell genomics

shiny-ggcorrplot2

An interactive Shiny App for correlation heatmap plots.

shiny-gggenes

An interactive Shiny App for drawing gene arrow maps.

shiny-upsetr

An interactive Shiny App for UpSet plots.

shixiangwang

Shixiang Wang' GitHub Profile

single-cell-data-visualization-tools

Collection of single-cell data visualization tools.

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"

snakepipes

A toolkit based on snakemake and python for analysis of NGS data

snaphic

SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data

snphylo

A pipeline to generate a phylogenetic tree from huge SNP data

speciestree

SpeciesTree is a useful tool to construct species trees using stringent single-copy nuclear genes across multiple species. It has been demonstrated to be useful in both plants and animals.

sprite-pipeline

A self-contained repository of all code needed for SPRITE analysis

st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

t_cell_signature_reference

tcr-bcr-seq-analysis

T/B cell receptor sequencing analysis notes

tomicsvis

Transcriptomics Visualization R package.