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/bioinformatics-workbook
Bioinformatics Workbook repository
molecules/English_Spanish_Dictionary
molecules/Bioinformatic_Tools
molecules/cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
molecules/cellranger-nf
nextflow pipeline for running cellranger
molecules/celltalker
Inference of cell-cell communication from single-cell RNAseq data
molecules/chronos
Modeling of time series data for CRISPR KO experiments
molecules/Cut_And_Run_Analysis_SnakeMake
Step-by-step instructions and Snakemake pipeline for processing Cut&Run data
molecules/Cytometry-R-scripts
R scripts to help with your flow cytometry analysis
molecules/DeepLabCut
Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans
molecules/FastQ-Screen
Detecting contamination in NGS data and multi-species analysis
molecules/genomepy
genes and genomes at your fingertips
molecules/imagej.github.io
The ImageJ wiki
molecules/muscat
Multi-sample multi-group scRNA-seq analysis tools
molecules/myproject
Testing workflowr
molecules/oddgenes
A small database of weird gene annotations
molecules/OSCA.intro
Introduction to the OSCA book.
molecules/Process_RepTiming_Snakemake
molecules/salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
molecules/SCISSORS
SCISSORS builds upon the Louvain graph-based clustering in Seurat by optimizing parameter selection when reclustering cell groups, with an eye towards identifying rare cell types.
molecules/scRNA.seq.course
Analysis of single cell RNA-seq data course
molecules/scRNAseq_Physalia_2022
snapshot of course as of 2022-06-13
molecules/seurat
R toolkit for single cell genomics
molecules/single-cell
Pipelines and scripts for single-cell best practices
molecules/single-cell-best-practices
https://www.sc-best-practices.org
molecules/Spectre
A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
molecules/style
The tidyverse style guide for R code
molecules/SynTracker
molecules/TIGAR
molecules/UniTVelo
UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference