yurasong Goto Github PK

10x-scatac-2019

Code Repository for Satpathy Granja et al 2019

atac-seq-pipeline

ENCODE ATAC-seq pipeline

awesome-single-cell

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

bioc2020workshop

biocnyc

Materials presented at the BiocNYC meet-up

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

cellphonedb

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

chromvarmotifs

R package with motifs for use with chromVAR

deeptools

Tools to process and analyze deep sequencing data.

imcsegmentationpipeline

A pixelclassification based multiplexed image segmentation pipeline

lollipops

Lollipop-style mutation diagrams for annotating genetic variations.

macs

MACS -- Model-based Analysis of ChIP-Seq

magic

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

mdlabbook

mdlabbook is a markdown-format lab notebook

midnight

Midnight is a Jekyll theme for GitHub Pages

ngs_course

Course on analysis of NGS data (RNA-Seq. and ATAC-Seq.) using Galaxy

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

nichenetr

NicheNet: predict active ligand-target links between interacting cells

posterdown

Use RMarkdown to generate PDF Conference Posters via HTML

powsimr

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

project-template

Template for project directory structure.

r-course_2021summer

r-coursework

R notebook and example data for beginner :)

seqtk

Toolkit for processing sequences in FASTA/Q formats

seurat

R toolkit for single cell genomics

severo.jl

a software package for analysis and exploration of single-cell RNA-seq datasets

thesis_academic

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms