jimmylijing Goto Github PK

abscnseq

AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data.

archive-datacarpentry

Data Carpentry workshop materials

atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

ballgown

Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.

ballgownrnaseq

chipseq_atacseq_pipelines

Snakemake pipelines for ChIPseq and ATACseq experiments

cnvkit

Copy number variant detection from targeted DNA sequencing

converting-mouse-to-human-gene-names-with-biomart-package

Converting mouse gene names to the human equivalent and vice versa is not always as straightforward as it seems, so I wrote a function to simplify the task. The function takes advantage of the getLDS() function from the biomaRt to get the hgnc symbol equivalent from the mgi symbol. For example, let’s convert the following mouse gene symbols, Hmmr, Tlx3, and Cpeb4, to their human equivalent.

excelerate-scrnaseq

Single RNA-seq data analysis with R (Finland, May, 2019)

ggplot2

hisat2

Graph-based alignment (Hierarchical Graph FM index)

integrate-neo

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

seurat

R toolkit for single cell genomics

star-fusion

STAR-Fusion codebase

stringtietodeseq2

varscan