SunmoonTao

pipx

Install and Run Python Applications in Isolated Environments

ploomber

The fastest ⚡️ way to build data pipelines. Develop iteratively, deploy anywhere. ☁️

elyra

Elyra extends JupyterLab with an AI centric approach.

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

scGPT

BI-BE-CS-183-2023

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

naas

Low-code Python library to safely use notebooks in production: schedule workflows, generate assets, trigger webhooks, send notifications, build pipelines, manage secrets (Cloud-only)

trgt

Tandem repeat genotyping and visualization from PacBio HiFi data

ChatGPT_Chemistry_Assistant

ChatGPT Chemistry Assistant

SCENT

Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA

RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.

CAFE_fig

A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)

RepeatHMM

a hidden Markov model to infer simple repeats from genome sequences

DeepRepeat

An accurate repeat detection from Nanopore data using deep learning and image techniques

NanoRepeat

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data

SHARE-seq-alignment

pipeline for demultiplex and align both ATAC and RNA data generated in SHARE-seq

multi_padlock_design

Padlock design pipeline for multiplexed assay with multiple probes per target in cDNA-based expression profiling

pyTanFinder

Python scripts to run tandem repeat finder program (Benson, 1999) and parse the results

genotyping-benchmarking

Snakemake-pipeline for benchmarking genotypers

VCFtoTree_1.0.0

Building phylogeny from 1000 Genome VCF file for 2504 individuals, also including ancient and primate genomes.

scRCAT-seq

Code for our scCAT-seq project

SOFTX-D-21-00195

NSDPY: A python package to download DNA sequences from NCBI. To cite this Original Software Publication: https://www.sciencedirect.com/science/article/pii/S235271102200036X

CSC509

For the CSC509 SFSU Course Deep Learning in Medical Imaging

Alubaster

Detection of novel Alu exonization events from RNA-seq data

vcf2tree

Create phylogenetic tree using whole genome sequencing data

ToverBoom

A python module to generate fancy multi-modal lineage trees

CopyKit-UserGuide

This is the User Guide for the CopyKit R Package

ml_microbiome_based_cancer_prediction

This project is a re-creation of the 2023 Nature paper "Machine learning‑based approaches for cancer prediction using microbiome data" by Freitas et. al.

C2_C3_training_data_performance