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learning-bioinformatics-at-home
resources for learning bioinformaticsJAuth
Java GUI client to generate Google authentication codesbioinformatics-coffee-hour
Short lessons from FAS Informatics coffee hourATAC-seq
snpArcher
Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.GenomeAnnotation
Best practices and workflow for genome annotationTranscriptomeAssemblyTools
A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.degenotate
micro-course
Code for Informatics nano coursespunnel
Spank TunnelsTranscriptomeAssemblyEvaluation
Workflows and scripts used to perform analyses for de novo transcriptome assembly manuscriptAnnotationTOGA
Guidelines for running TOGA and scripts for processing outputsscrub-jay-genomics
website
Website markdown filesPandAnnotate
A python-based alternative to Trinotate for merging herterogeneous transcriptome assembly annotation tablesspecify_web
Conversion of HUH specify_web application to gitinfoscripts
ifxdjango
Django project template for ifx Django REST / VueJS / Vuetify applicationsGenomeAnnotation-WholeGenomeAlignment
guidelines for running progressive CACTUS to produce a whole genome alignment required for genome annotation tools that leverage WGAGenomeAnnotation-Maker
Guidelines for running MAKERnanopore-assembly
imagej_processing
Demo files for ImageJ (headless) macro processing and SLURM scripts for Office Hours/Tips at 12econ
Economic botany applicationpython-workshop
Python workshop materialsiggybase
iggybase is a general database frontend. First, we are rolling it out as Laboratory Information Management System (LIMS).bulk_RNA-seq
Best practices, scripts and workflows for performing bulk RNA-seq expression analysesGenomeAnnotation-ComparativeAugustus
Guidelines for running multi-genome AUGUSTUS, and scripts for processing outputsrcsqueue
bioblog
Useful bioinformatics scriptsBulkRNAseq2Counts
A Snakemake workflow for generating expression count tables from either locally stored fastq files or NCBI-SRA accessions for bulk RNA-seqAnnotationBRAKER
Workflows and code for generating and filtering genome annotations with BRAKERratites
Code for Scott Edwards ratite grant.specify_rapid
Rapid data upload tool for specify. Conversion from SVN.minilimsdb
The database component for MiniLIMS. Used for containerization.GenomeAnnotation-Braker
Guidelines for running BRAKER, and scripts for processing outputshex
Shell command APIspecify-huh
git version of the HUH specify svn repoPhyloAcc-interface
Front-end for PhyloAccintro-to-bwa
Informatics Coffee Hour demoquantproteomics
harvard_doc
Standalone application for creating Harvard-branded PDFsAnnotationRNAseqAssembly
Snakemake workflow for assembling transcript models from RNA-seq readsLove Open Source and this site? Check out how you can help us