Pinned Repositories
abstar
VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.
AnnotationPipeline-EVM_based-DClab
Cantù Lab @ UC Davis - Annotation pipeline - EVM based
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
BAMreport
Report on a BAM file
bioinformatics
this is a hub for bioinformatics
chip-seq-pipeline2
ENCODE ChIP-seq pipeline
Chromatin_Analysis_2020_cell
Source codes and example scripts for chromatin tracing projects in Zhuang lab
cov2tree
Cov2Tree website, based on Taxodium
covtobed
⛰ covtobed | Convert the coverage track from a BAM file into a BED file
google-research
Google Research
shulp2211's Repositories
shulp2211/alphafold
Open source code for AlphaFold.
shulp2211/atac-seq-pipeline
ENCODE ATAC-seq pipeline
shulp2211/cellBrowser
Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
shulp2211/CHM13
The complete sequence of a human genome
shulp2211/covariants
Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.
shulp2211/covizu
Rapid analysis and visualization of coronavirus genome variation
shulp2211/cuteSV
Long read based human genomic structural variation detection with cuteSV
shulp2211/deeplearning-biology
A list of deep learning implementations in biology
shulp2211/guppy
🐠A friendly application manager and task runner for React.js
shulp2211/ilus
A handy pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
shulp2211/InfiniteSites
Simulator and analysis of Infinite Sites Assumption breakdown
shulp2211/intro-to-deepcell
An introduction to deepcell and deep learning
shulp2211/jbrowse
A modern genome browser built with JavaScript and HTML5.
shulp2211/kraken2
The second version of the Kraken taxonomic sequence classification system
shulp2211/MERINGUE
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
shulp2211/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
shulp2211/mlst
:id: Scan contig files against PubMLST typing schemes
shulp2211/nextclade
Viral genome alignment, clade assignment, mutation calling, and quality checks
shulp2211/pan-genome-visualization
shulp2211/pangolin
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
shulp2211/performance
:muscle: Models' quality and performance metrics (R2, ICC, LOO, AIC, BF, ...)
shulp2211/prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
shulp2211/RoseTTAFold
This package contains deep learning models and related scripts for RoseTTAFold
shulp2211/rust-bio-tools
A set of command line utilities based on Rust-Bio.
shulp2211/SandDance
Visually explore, understand, and present your data.
shulp2211/SARS-CoV-2_Sequencing
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
shulp2211/shasta
De novo assembly from Oxford Nanopore reads.
shulp2211/smoove
structural variant calling and genotyping with existing tools, but, smoothly.
shulp2211/STAR
RNA-seq aligner
shulp2211/Ventoy
A new bootable USB solution.