SunmoonTao

CSC509

For the CSC509 SFSU Course Deep Learning in Medical Imaging

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

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)

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.

genotyping-benchmarking

Snakemake-pipeline for benchmarking genotypers

C2_C3_training_data_performance

scGPT

SCENT

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

BI-BE-CS-183-2023

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

pipx

Install and Run Python Applications in Isolated Environments

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

RepeatHMM

a hidden Markov model to infer simple repeats from genome sequences

ToverBoom

A python module to generate fancy multi-modal lineage trees

ChatGPT_Chemistry_Assistant

ChatGPT Chemistry Assistant

SHARE-seq-alignment

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

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

multi_padlock_design

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

CAFE_fig

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

VCFtoTree_1.0.0

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

vcf2phylip

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

vcf2tree

Create phylogenetic tree using whole genome sequencing data

trgt

Tandem repeat genotyping and visualization from PacBio HiFi data

CopyKit-UserGuide

This is the User Guide for the CopyKit R Package

scRCAT-seq

Code for our scCAT-seq project

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.

Alubaster

Detection of novel Alu exonization events from RNA-seq data

ploomber

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

elyra

Elyra extends JupyterLab with an AI centric approach.

pyTanFinder

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