A small R package to make sequencing read coverage plots in R.

A tool for bigWig files.

Generate IGV style locus tracks from bigWig files in R

Generate IGV style locus tracks from bigWig files in R

Codeine is a Python library for constrained reverse translation of protein sequences.

A mapper for 10x-flex single cell sequencing reads with fixed abstract geometries

hypergeometric testing of guide RNA identity to assign cell barcodes to a guide identity

Draw RNA secondary structures in python.

A python package for simultaneous Hyperparameters Tuning and Features Selection for Gradient Boosting Models.

Ark, an R kernel

mouse & keyboard sharing via LAN

We provide pytorch training scripts for enformer and borzoi

Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of regulatory elements.

Bash wrapper for simple set operations using sort and uniq

An interactive explorer for single-cell transcriptomics data

LLM agents for working with the SRA and associated bioinformatics databases.

This repo contains accompanying code for the miRBench benchmarking approach.

Repository for the Anczukow-Lab splicing pipeline

Nanopore sequence read simulator

[G]enomic [P]ositioning with [Py]thon

Lightweight, performant, deep table extraction

Scientific Document Insight Q/A

Local PDF Chat Application with Mistral 7B LLM, Langchain, Ollama, and Streamlit

ERVmap is one part curated database of human proviral ERV loci and one part a stringent algorithm to determine which ERVs are transcribed in their RNA seq data.

fastest GTF/GFF-to-BED converter chilling around