Pinned Repositories
bashpack
My current .bashrc and vim configurations
Bio--SNP--Inherit
This is a module for converting Single Nucleotide Polymorphism (SNP) genotype data to parental allele designations. This helps with creating files suitable for mapping, identifying and characterizing crossovers, and also helps with quality control.
Bio-IRCF-FASTQ-Tiny
FASTQ iterator designed to be much faster and much more flexible than using BioPerl
bioinformatics-workbook
Bioinformatics Workbook repository
English_Spanish_Dictionary
GBrowseConfigStrict
Prepare selected lines from GBrowse config for syntax checking, including strictures and warnings. Intended for use with Vim.
p6-wrapper-for-p5-cat
Example of wrapping up a Perl 5 script in a Perl 6 module
Perl6-misc
Some of my miscellaneous Perl 6 scripts
sarray_script
Create shell scripts that process whole directories of files using SLURM arrays. Also works for paired files (like paired-end FASTQ files).
smcpp
SMC++ infers population history from whole-genome sequence data.
molecules's Repositories
molecules/bashpack
My current .bashrc and vim configurations
molecules/sarray_script
Create shell scripts that process whole directories of files using SLURM arrays. Also works for paired files (like paired-end FASTQ files).
molecules/atlas
ATLAS - Three commands to start analysing your metagenome data
molecules/bio
Bioinformatics utilities.
molecules/biocompute_git_branch_example
molecules/BioinformaticsResources
molecules/book
molecules/Cecret
Nextflow workflow for our analysis of SARS-COV-2
molecules/clone_reducer
Clone reducing script used in Estep et al. (2014).
molecules/create_matrix_from_star_gene_count_files
Create matrix suitable for DeSeq2 file from Star gene count files
molecules/csvkit
A suite of utilities for converting to and working with CSV, the king of tabular file formats.
molecules/demo_seqs
molecules/Dist-Zilla
scary tools for building CPAN distributions
molecules/dist-zilla-plugin-changelogfromgitsiimple
molecules/dzp-changelogfromgit
Dist::Zilla plugin to generate changelogs from git commits
molecules/for_puzzles
molecules/Git-Examples
molecules/Hello-world
molecules/hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
molecules/Intro-to-rnaseq-hpc-O2
This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster
molecules/migec
A RepSeq processing swiss-knife
molecules/Miscellaneous-Python-Scripts
molecules/multi_tsv_to_xlsx
molecules/nextclade
Assign SARS-CoV-2 clades in the browser
molecules/p6-concurrent-queue
A lock-free concurrent queue data structure.
molecules/RNA-Seq-Toolkit-old
Collection of scripts to facilitate the analysis of RNA-Seq data
molecules/rnaseq-nf
A proof of concept of RNAseq pipeline
molecules/single-cell-ircf
Single cell scripts from MU's IRCF
molecules/slurm
Slurm: A Highly Scalable Workload Manager
molecules/staphb_toolkit
Python Toolkit for using containerized programs in either Singularity or Docker