jd-campbell

LLMsPracticalGuide

A curated list of practical guide resources of LLMs (LLMs Tree, Examples, Papers)

statements

Successful Job Applications and Grants

ontogpt

LLM-based ontological extraction tools, including SPIRES

AGAT

Another Gtf/Gff Analysis Toolkit

BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

datasets

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

jekyll-twitter-plugin

A Liquid tag plugin for the Jekyll blogging engine that embeds Tweets, Timelines and more from Twitter API

GENESPACE

data-primers

GFF3toolkit

Python programs for processing GFF3 files

COPILOT

Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline as the input of copilot.

divbrowse

A web application for interactive visualization and exploratory data analysis of variant call matrices

B3

Biodiversity Genomics Academy 2023: Gene prediction with BRAKER3

pandagma

Generate pan-gene sets, given a collection of genome assemblies and corresponding gene models.

Fill-gaps-manually

How to fill gaps in genome of soybean

jekyll-legumeinfo

legumeinfo.org built with Jekyll and served on GitHub Pages

braker

braker container

conda_demo

demonstrate conda environment

Funnotate

Functional annotation of FASTA sequences

issueMigratorPro

Issue Migrator Pro is a very well (typescript) script to move and close issues in GitHub repos - very handy when you are splitting up repos and projects

jekyll-soybase

SoyBase site, forked from jekyll-legumeinfo mid-2022; built with Jekyll and served on GitHub Pages

SEA_paper

Code and data associated with the paper 'The Soybean Expression Atlas v2: a comprehensive database of over 5000 RNA-seq samples'

SoybeanAtlas_issues

A repo to report issues on the Soybean Expression Atlas database.

kmer_masked_annotation

annotation pipeline based on kmasker and braker2

work_php

AHRD-not-HARD

a bit of wrapper for running the AHRD analysis in "standalone" mode (ie not via the web interface)

datastore-registry

Registry of unique KEY4 keys and their associated Genus-species-collection information

SoyMeta

Large scale meta-analysis of soybean

SoyBase

Scripts to suck data out of the SoyBase MySQL database for loading into the mines (and upload to the LIS datastore)

breedbase.R

An R package that helps generate breeDBase upload templates