JimmyLiJing's repositories
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.
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)
hisat2
Graph-based alignment (Hierarchical Graph FM index)
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