Explore @harvardinformatics Open Source projects

Harvard Informatics (@harvardinformatics)

harvardinformatics

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learning-bioinformatics-at-home

resources for learning bioinformatics

JAuth

Java GUI client to generate Google authentication codes

bioinformatics-coffee-hour

Short lessons from FAS Informatics coffee hour

ATAC-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 annotation

TranscriptomeAssemblyTools

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 course

spunnel

TranscriptomeAssemblyEvaluation

Workflows and scripts used to perform analyses for de novo transcriptome assembly manuscript

AnnotationTOGA

Guidelines for running TOGA and scripts for processing outputs

scrub-jay-genomics

website

Website markdown files

PandAnnotate

A python-based alternative to Trinotate for merging herterogeneous transcriptome assembly annotation tables

specify_web

Conversion of HUH specify_web application to git

infoscripts

ifxdjango

Django project template for ifx Django REST / VueJS / Vuetify applications

GenomeAnnotation-WholeGenomeAlignment

guidelines for running progressive CACTUS to produce a whole genome alignment required for genome annotation tools that leverage WGA

GenomeAnnotation-Maker

Guidelines for running MAKER

nanopore-assembly

imagej_processing

Demo files for ImageJ (headless) macro processing and SLURM scripts for Office Hours/Tips at 12

econ

Economic botany application

python-workshop

Python workshop materials

iggybase

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 analyses

pacbio_hifi_assembly

A snakemake workflow for assembly with HiFi

GenomeAnnotation-ComparativeAugustus

Guidelines for running multi-genome AUGUSTUS, and scripts for processing outputs

rcsqueue

bioblog

Useful bioinformatics scripts

BulkRNAseq2Counts

A Snakemake workflow for generating expression count tables from either locally stored fastq files or NCBI-SRA accessions for bulk RNA-seq

AnnotationBRAKER

Workflows and code for generating and filtering genome annotations with BRAKER

ratites

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 outputs

hex

Shell command API

specify-huh

git version of the HUH specify svn repo

PhyloAcc-interface

Front-end for PhyloAcc

intro-to-bwa

Informatics Coffee Hour demo

Jupyter Notebook

quantproteomics

harvard_doc

Standalone application for creating Harvard-branded PDFs

AnnotationRNAseqAssembly

Snakemake workflow for assembling transcript models from RNA-seq reads