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bam2fastq-nf

nextflow pipeline to convert uBAMs to fastq using samtools, run fastqc and produce a multiqc report

bamtofastq

book

burgertools

Bundle of Useful scRNA-seq Gating Tools Extending seuRat

car-t-image-analysis

chat-with-github-repo

This repository contains two Python scripts that demonstrate how to create a chatbot using Streamlit, OpenAI GPT-3.5-turbo, and Activeloop's Deep Lake.

chatbot-ui

The open-source AI chat interface for everyone.

colonmesenchymescrnaseq

Analysis of 10x scRNA-Seq of human and murine colonic stromal cell transcriptomic data in health in IBD

configs

Config files used to define parameters specific to compute environments at different Institutions

datasciencewithpython

Learn Data Science with focus on adding value with the most efficient tech stack.

dge

Nextflow pipeline that runs DESeq2 on data processed with the nextflow RNAseq pipeline

dsbook

Repository for data science book

helpers

Personal Package for Denis O'Meally

jupyterhub

jupyterlab-sos

k8-cluster-in-proxmox

Deploying a Kubernetes cluster using Terraform

litellm

Call all LLM APIs using the OpenAI format. Use Bedrock, Azure, OpenAI, Cohere, Anthropic, Ollama, Sagemaker, HuggingFace, Replicate (100+ LLMs)

manuscript-shared-rnaseq

R and Rmarkdown code used across multiple RNA-Seq projects.

mlflow-docker-compose

MLflow deployment with 1 command

pfb2019

Programming for Biology 2019

r-bioinformatics-cookbook

R Bioinformatics Cookbook, published by Packt

rstudio-rbioc

sanbomics_scripts

scripts and notebooks from sanbomics

sccity

What the Package Does (One Line, Title Case)

scrnaseq

Workflow for single-cell RNA-seq analysis using Seurat

selex-nf

Nextflow pipeline for SELEX library QC and enrichment analysis

singlecellsequencinginr

Some useful R scripts for some genomics graphing

slurm-cluster

Docker local slurm cluster

smrnaseq

A small-RNA sequencing analysis pipeline

stats

Tools that speed up statistical analysis using command line