Pinned Repositories
ATAC-seq
bioinformatics-coffee-hour
Short lessons from FAS Informatics coffee hour
degenotate
GenomeAnnotation
Best practices and workflow for genome annotation
JAuth
Java GUI client to generate Google authentication codes
learning-bioinformatics-at-home
resources for learning bioinformatics
NGmerge
Merging paired-end reads and removing adapters
snpArcher
Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
spunnel
Spank Tunnels
TranscriptomeAssemblyTools
A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.
Harvard Informatics's Repositories
harvardinformatics/snpArcher
Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
harvardinformatics/GenomeAnnotation
Best practices and workflow for genome annotation
harvardinformatics/TranscriptomeAssemblyTools
A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.
harvardinformatics/degenotate
harvardinformatics/AnnotationTOGA
Guidelines for running TOGA and scripts for processing outputs
harvardinformatics/scrub-jay-genomics
harvardinformatics/website
Website markdown files
harvardinformatics/ifxdjango
Django project template for ifx Django REST / VueJS / Vuetify applications
harvardinformatics/specify_web
Conversion of HUH specify_web application to git
harvardinformatics/AnnotationBRAKER
Workflows and code for generating and filtering genome annotations with BRAKER
harvardinformatics/BulkRNAseq2Counts
A Snakemake workflow for generating expression count tables from either locally stored fastq files or NCBI-SRA accessions for bulk RNA-seq
harvardinformatics/pacbio_hifi_assembly
A snakemake workflow for assembly with HiFi
harvardinformatics/AnnotationRNAseqAssembly
Snakemake workflow for assembling transcript models from RNA-seq reads
harvardinformatics/specify_rapid
Rapid data upload tool for specify. Conversion from SVN.
harvardinformatics/djvocab
Vocabulary table for Django
harvardinformatics/github-intro
A hands-on introduction to git/github
harvardinformatics/ifxurls
Tools for getting urls in the ifx environment
harvardinformatics/ifxvue
Harvard FAS Informatics Vue JS components
harvardinformatics/informatics-website
FAS Informatics website
harvardinformatics/AllAsia-Symbiota
The Symbiota Virtual Flora/Fauna project is an open source software project, with central goal of developing on-line tools that aid in the generation, exploration and management of biodiversity data (collection specimens, observations, images, checklist, keys, etc.). See also: http://bdj.pensoft.net/articles.php?id=1114 and http://symbiota.org/
harvardinformatics/bioconda-recipes
Conda recipes for the bioconda channel.
harvardinformatics/bird-dfe
harvardinformatics/cnstoolsearch
harvardinformatics/django-cas-server
A Django Central Authentication Service server implementing the CAS Protocol 3.0 Specification
harvardinformatics/EndoriftiaTranscriptomics
Code used in data analysis for Mitchell et al. 2024, a forthcoming paper on transcriptomic responses to environmental variation in *Candidatus Endoriftia persephone*, a bacterial symbiont of the deep sea tubeworm *Riftia pachyptila*.
harvardinformatics/IP4CI
IP4CI: an interpretable pathway-based computational method for cross-species cell-type identification from single cell data
harvardinformatics/Mapping-simulations
Read mapping simulations while varying divergence levels
harvardinformatics/mop
Simple tool for capturing alignment regions with sufficient quality for genotyping.
harvardinformatics/parse-pileup
harvardinformatics/PEA