orangeSi

myth's repositories

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

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pymsaploter

plot Multiple Sequence Alignment(MSA) of Clustal by python package

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bam2msa

convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region

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tinypandas

easy-to-use data structures and data analysis tools ( still be in draft, inspired by Python Pandas )

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biokits

bioinformatics tools

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grepfile

a alternative for $grep -f A.list B.list which cost too many memory and time

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doi2scihub

a simple chrome extension for navigate to scihub by doi

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biowasm

WebAssembly modules for genomics

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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.

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PAMpredict

A python package to predict CRISPR-Cas PAMs

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pygtrait

genome chromosome traits or marker annotation plot

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AlphaFold3

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

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AutoViz

Automatically Visualize any dataset, any size with a single line of code. Created by Ram Seshadri. Collaborators Welcome. Permission Granted upon Request.

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