dence

anything-llm

The all-in-one Desktop & Docker AI application with built-in RAG, AI agents, and more.

unsloth

Finetune Llama 3.2, Mistral, Phi, Qwen 2.5 & Gemma LLMs 2-5x faster with 80% less memory

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

goatools

Python library to handle Gene Ontology (GO) terms

statements

Successful Job Applications and Grants

GSEApy

Gene Set Enrichment Analysis in Python

pilon

Pilon is an automated genome assembly improvement and variant detection tool

funannotate

Eukaryotic Genome Annotation Pipeline

sgkit

Scalable genetics toolkit

cmapPy

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools

flo

Same species annotation lift over pipeline.

genotype_plot

A set of functions to visualise genotypes based on a VCF

ggPlantmap

bigg_models

The BiGG Models website server

pyComBat

pyComBat is a Python 3 implementation of ComBat, one of the most widely used tool for correcting technical biases, called batch effects, in microarray expression data.

deconv_benchmark

LRSIM

10x Genomics Reads Simulator

appliedgenomics2023

Materials for EN.601.449/649 Computational Genomics: Applied Comparative Genomics

NLRtracker

NLR annotation tool

KEGGscape

A Cytoscape app for importing KGML(KEGG pathway XML)

nextflow-template-repository

GitHub template repository for creating new barebones Nextflow pipelines, using the Arcadia-Science/nextflow-template cookiecutter template

GNPS_MASST

ibdplexus

This package helps wrangle the clinical data in IBD Plexus. IBD Plexus is a data exchange platform designed to accelerate research toward finding cures for Inflammatory Bowel Disease (IBD). To learn more please see https://www.crohnscolitisfoundation.org/research/current-research-initiatives/ibd-plexus.

IsoSeqSim

Iso-Seq reads simulator for PacBio and ONT full-length isoform sequencing technologies

transcriptome_assembly

Biocore's de novo transcriptome assembly workflow based on Nextflow

biopython

Official git repository for Biopython (converted from CVS)

MiscGenomicsTools

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