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yanhong hong (HongYhong)

HongYhong

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yanhong hong's starred repositories

biocode

Bioinformatics code libraries and scripts

Language:PythonLicense:MITStargazers:467Issues:0Issues:0

FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data

Language:JavaLicense:NOASSERTIONStargazers:167Issues:0Issues:0

granges

A Rust library and command line tool for working with genomic ranges and their data.

Language:RustStargazers:87Issues:0Issues:0

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

Language:PythonLicense:BSD-3-ClauseStargazers:1146Issues:0Issues:0

GENESPACE

Language:RLicense:NOASSERTIONStargazers:174Issues:0Issues:0

evo

DNA foundation modeling from molecular to genome scale

Language:Jupyter NotebookLicense:Apache-2.0Stargazers:827Issues:0Issues:0

DNA-Diffusion

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

Language:Jupyter NotebookLicense:NOASSERTIONStargazers:349Issues:0Issues:0

Isosceles

The Isoforms from Single-Cell; Long-read Expression Suite

Language:RLicense:GPL-3.0Stargazers:11Issues:0Issues:0

infernal

RNA secondary structure/sequence profiles for homology search and alignment

Language:CLicense:NOASSERTIONStargazers:99Issues:0Issues:0

BamSlam

Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files

Language:RLicense:MITStargazers:11Issues:0Issues:0

spycone

Spicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data

Language:PythonLicense:GPL-3.0Stargazers:10Issues:0Issues:0

findpeaks

The detection of peaks and valleys in a 1d-vector or 2d-array (image)

Language:PythonLicense:NOASSERTIONStargazers:212Issues:0Issues:0

rnavar

gatk4 RNA variant calling pipeline

Language:NextflowLicense:MITStargazers:31Issues:0Issues:0

long-read-pipelines

Long read production pipelines

Language:Jupyter NotebookLicense:BSD-3-ClauseStargazers:123Issues:0Issues:0

parallel-disk-usage

Highly parallelized, blazing fast directory tree analyzer

Language:RustLicense:Apache-2.0Stargazers:358Issues:0Issues:0

scnanoseq

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

Language:NextflowLicense:MITStargazers:5Issues:0Issues:0

figeno

Tool for plotting sequencing data along genomic coordinates.

Language:PythonLicense:GPL-3.0Stargazers:160Issues:0Issues:0

FEELnc

FEELnc : FlExible Extraction of LncRNA

Language:PerlLicense:GPL-3.0Stargazers:77Issues:0Issues:0

vireo

Demultiplexing pooled scRNA-seq data with or without genotype reference

Language:PythonLicense:Apache-2.0Stargazers:67Issues:0Issues:0

fq

Command line utility for manipulating Illumina-generated FASTQ files.

Language:RustLicense:MITStargazers:67Issues:0Issues:0

pytorch-doc-zh

Pytorch 中文文档

Language:ShellStargazers:4060Issues:0Issues:0

mudskipper

A tool for projecting genomic alignments to transcriptomic coordinates

Language:RustLicense:BSD-3-ClauseStargazers:30Issues:0Issues:0

drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

Language:PythonLicense:MITStargazers:127Issues:0Issues:0

LongReadBenchmark

Benchmarking long-read RNA-seq analysis tools

Language:RLicense:MITStargazers:23Issues:0Issues:0

squigulator

a tool for simulating nanopore raw signal data

Language:CLicense:MITStargazers:57Issues:0Issues:0

nanopack

An overview of all nanopack tools

Language:PythonLicense:GPL-3.0Stargazers:199Issues:0Issues:0

LexicHash

A novel method for sequence similarity estimation

Language:PythonStargazers:21Issues:0Issues:0

chopper

Language:RustLicense:MITStargazers:126Issues:0Issues:0

nanofilt

Filtering and trimming of long read sequencing data

Language:PythonLicense:GPL-3.0Stargazers:181Issues:0Issues:0

pbmm2

A minimap2 frontend for PacBio native data formats

Language:PerlLicense:BSD-3-Clause-ClearStargazers:165Issues:0Issues:0