johnsilenin Goto Github PK

bioinfo_pipeline

Bioinformatics pipeline for QC, alignment, variant calling and visualization of NGS data.

bioinformatic-resources

datascience-bioinformatics

Different tasks from the field of data science applied on typical bioinformatic data. Mainly used packages are numpy and scipy and the code is organized in jupyter notebooks.

denovo-assembly-tutorial

A tutorial for learning de novo assembly

gbs

Pipeline for GBS data.

metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

microbiomeexplorer

The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.

panda

genomics pathway visualization tool

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

qiime2r

Import qiime2 artifacts to R

r-for-data-science-lunchbreak-lessons

Source files for the LinkedIn Learning Course

rna-seq-analysis

RNAseq analysis notes from Tommy Tang

sampleproject

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.

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"

wes-pipeline