hpcbio Goto Github PK

iforgegenomegps

version of MayoGenomeGPS for the iforge system at NCSA

imtornado2

Illinois Mayo Taxonomy Operations for RNA Database Operations

in-depth-ngs-data-analysis-course

Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.

intro-to-chipseq

Intro to ChIPseq using HPC

intro-to-linux

klib-xs

Perl XS bindings to Klib

kraken

Kraken taxonomic sequence classification system

lifescitrainingslack

A Slack community of people who do short-format training in the life sciences

managing_batch_effects

mayo-genome-assembly

mayo-rnaseq

Scripts for RNA-Seq module of Computational Genomics Course

mayo-variant-calling

Basic scripts for the Mayo-Illinois course

medips-bioc

BioC copy of MEDIPS, will have a branch to include small changes from Herb-Shook project

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

methylseq-old

Old copy of the nf-core methylseq workflow including hacked in NuGen/Tecan support

microbial-profiling

HPCBio's Microbial Profiling Analysis workshop page

microbiomeexperiment

Bioconductor defining a summarizedExperiment class (metagenomeSE) for metagenomic data.

mirna-sample-tracker

Simple miRNA-oriented read/sample/database tracker

mite-hunter

msar

The BioJS MSA viewer wrapped into an R package

mvp

An implementation of Mass spectrometry Data Preprocessor in R Edit

nbisweden-pipelines-nextflow

NBIS nextflow pipelines framework

nextflow-training

Nextflow training material

nudup

NuDup -- Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.

numetrrbs

ont-assembly-polish

ONT assembly and Illumina polishing pipeline

organization-genomics

Lesson on data organization and project setup for genomics

phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

phyloseq-extended

Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" provided by the platforms Migale and Genotoul

plotly_microbiome

R helper functions for making Plotly graphs in microbiome work