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intro-to-rnaseq-hpc-salmon

jamba

Jam Base Methods for R

machinelearning_notes

Machine learning and deep learning resources

mofa_analysis

Scripts to analyse CLL data in MOFA paper

monkparakeet

chromosome assembly and neo-sex chromosome of monk parakeet

myfunctions

Collection of custom R functions

pyflow-atacseq

ATAC-seq snakemake pipeline

pyflow-chipseq

a snakemake pipeline to process ChIP-seq files from GEO or in-house

pygtftk

A python package and a set of shell commands to handle GTF files

python-100-days

Python - 100天从新手到大师

r_notes

Data science in R notes

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

scenic

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

scrna-seq-workshop

single cell RNA-seq analysis workshop

scrna-seq_notes

A list of scRNA-seq analysis tools

scrna_10x

seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

seqan

SeqAn's official repository.

seurat-to-rna-velocity

A guide to using a Seurat object in conjunction with RNA Velocity

single-cell-rnaseq-analysis

A guide for analyzing single-cell RNA-seq data using the R package Seurat. Go from raw data to cell clustering, identifying cell types, custom visualizations, and group-wise analysis of tumor infiltrating immune cells using data from Ishizuka et al. Nature 2019.

single_cell_airway

R code for single-cell analysis of airway epithelial cells

single_cell_intestine

R code for single-cell analysis of intestinal epithelial cells

snakefiles

:snake: Snakefiles for common RNA-seq data analysis workflows.

tcrseq

Reconstruction of T cell receptor sequences from single-cell RNA-seq data.

tools-devteam

Contains a set of Galaxy Tools mostly written by the Galaxy Team.

training-material

A collection of Galaxy-related training material

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

tutorials

:books: Various bioinformatics tutorials

ubccr_docs

CCR's research computing documentation