https://www.sc-best-practices.org

Formalizing and benchmarking open problems in single-cell genomics

For the CSC509 SFSU Course Deep Learning in Medical Imaging

Deep probabilistic analysis of single-cell and spatial omics data

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

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.

Snakemake-pipeline for benchmarking genotypers

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

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

Install and Run Python Applications in Isolated Environments

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

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

a hidden Markov model to infer simple repeats from genome sequences

A python module to generate fancy multi-modal lineage trees

ChatGPT Chemistry Assistant

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

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

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

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

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

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

Create phylogenetic tree using whole genome sequencing data

Tandem repeat genotyping and visualization from PacBio HiFi data

This is the User Guide for the CopyKit R Package

Code for our scCAT-seq project

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 belo…

Detection of novel Alu exonization events from RNA-seq data

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