orangeSi
bioinformatic bird flying in microbial genomics of BGI ShenZhen in China
ReforgeneChina,GuangZhou
Pinned Repositories
bam2msa
convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region
bin
some small script in bioinformatics
biokits
bioinformatics tools
doi2scihub
a simple chrome extension for navigate to scihub by doi
grepfile
a alternative for $grep -f A.list B.list which cost too many memory and time
GSSplayground
Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature
ISfinder_database
download isfinder database
pymsaploter
plot Multiple Sequence Alignment(MSA) of Clustal by python package
rr
a simple bookmark tool by crystal-lang in command line of terminal for lazy guy in Linux
tinypandas
easy-to-use data structures and data analysis tools ( still be in draft, inspired by Python Pandas )
orangeSi's Repositories
orangeSi/GSSplayground
Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature
orangeSi/pymsaploter
plot Multiple Sequence Alignment(MSA) of Clustal by python package
orangeSi/bam2msa
convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region
orangeSi/tinypandas
easy-to-use data structures and data analysis tools ( still be in draft, inspired by Python Pandas )
orangeSi/biokits
bioinformatics tools
orangeSi/grepfile
a alternative for $grep -f A.list B.list which cost too many memory and time
orangeSi/doi2scihub
a simple chrome extension for navigate to scihub by doi
orangeSi/biowasm
WebAssembly modules for genomics
orangeSi/muscle
Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
orangeSi/PAMpredict
A python package to predict CRISPR-Cas PAMs
orangeSi/pygtrait
genome chromosome traits or marker annotation plot
orangeSi/AlphaFold3
Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
orangeSi/AutoViz
Automatically Visualize any dataset, any size with a single line of code. Created by Ram Seshadri. Collaborators Welcome. Permission Granted upon Request.
orangeSi/awesome-bioinformatics-crystal
orangeSi/awesome-CRISPR
List of software/websites/databases/other stuff for genome engineering
orangeSi/CRISPRtracrRNA
orangeSi/CrysDA
Crystal library for Data Analysis, Wrangling, Munging
orangeSi/crystal
The Crystal Programming Language
orangeSi/jgi-query
A simple command-line tool to download data from the Joint Genome Institute's database
orangeSi/lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
orangeSi/LRS_SV_sets
VCF files of SVs using long-read sequencing (LRS).
orangeSi/markd
Yet another markdown parser, Compliant to CommonMark specification, written in Crystal.
orangeSi/num.cr
Scientific computing in pure Crystal
orangeSi/OpenCRISPR
AI-generated gene editing systems
orangeSi/panel
A high-level app and dashboarding solution for Python
orangeSi/pdbe-molstar
Molstar PDBe implementation
orangeSi/python-mastery
Advanced Python Mastery (course by @dabeaz)
orangeSi/syntaxer
Multi-backend syntax highlighter for Crystal
orangeSi/TrimGalore
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
orangeSi/wasmer-crystal
WebAssembly runtime for Crystal