Liming Tao (SunmoonTao)

SunmoonTao

Geek Repo

Company:Broad Institute

Location:Cambridge, MA

Github PK Tool:Github PK Tool

Liming Tao's starred repositories

pipx

Install and Run Python Applications in Isolated Environments

Language:PythonLicense:MITStargazers:10427Issues:76Issues:793

ploomber

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

Language:PythonLicense:Apache-2.0Stargazers:3509Issues:30Issues:866

elyra

Elyra extends JupyterLab with an AI centric approach.

Language:PythonLicense:Apache-2.0Stargazers:1849Issues:45Issues:1620

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

Language:PythonLicense:BSD-3-ClauseStargazers:1236Issues:26Issues:1033
Language:Jupyter NotebookLicense:MITStargazers:1024Issues:33Issues:233

BI-BE-CS-183-2023

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

Language:Jupyter NotebookLicense:NOASSERTIONStargazers:436Issues:9Issues:3

vcf2phylip

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

Language:PythonLicense:GPL-3.0Stargazers:291Issues:9Issues:47

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)

Language:PythonLicense:AGPL-3.0Stargazers:285Issues:4Issues:186

trgt

Tandem repeat genotyping and visualization from PacBio HiFi data

Language:RustLicense:NOASSERTIONStargazers:103Issues:30Issues:43

ChatGPT_Chemistry_Assistant

ChatGPT Chemistry Assistant

Language:Jupyter NotebookStargazers:70Issues:2Issues:2

SCENT

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

Language:RLicense:NOASSERTIONStargazers:66Issues:14Issues:9

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

Language:PythonLicense:NOASSERTIONStargazers:34Issues:17Issues:57

DeepRepeat

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

Language:CLicense:NOASSERTIONStargazers:20Issues:7Issues:13

NanoRepeat

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

Language:PythonLicense:MITStargazers:15Issues:11Issues:14

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

Language:PythonLicense:MITStargazers:13Issues:4Issues:10

pyTanFinder

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

genotyping-benchmarking

Snakemake-pipeline for benchmarking genotypers

Language:PythonStargazers:8Issues:1Issues:0

VCFtoTree_1.0.0

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

Language:PythonStargazers:5Issues:3Issues:0

scRCAT-seq

Code for our scCAT-seq project

Language:RStargazers:5Issues:0Issues:0

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

Language:PythonLicense:MITStargazers:4Issues:0Issues:0

CSC509

For the CSC509 SFSU Course Deep Learning in Medical Imaging

Language:Jupyter NotebookStargazers:4Issues:1Issues:0

Alubaster

Detection of novel Alu exonization events from RNA-seq data

Language:PerlLicense:GPL-3.0Stargazers:4Issues:1Issues:0

vcf2tree

Create phylogenetic tree using whole genome sequencing data

Language:ShellLicense:Apache-2.0Stargazers:3Issues:2Issues:0

ToverBoom

A python module to generate fancy multi-modal lineage trees

Language:Jupyter NotebookStargazers:2Issues:2Issues:6

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.

Language:Jupyter NotebookStargazers:1Issues:0Issues:0
Language:Jupyter NotebookStargazers:1Issues:0Issues:0