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amit yadav's starred repositories

pb-metagenomics-tools

Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics

Language:HTMLBSD-3-Clause-Clear15600

reference

⭕ Share quick reference cheat sheet for developers.

Language:EJSGPL-3.0569900

dot

Dot: An interactive dot plot viewer for comparative genomics

Language:JavaScriptMIT3100

clinker

Gene cluster comparison figure generator

Language:PythonMIT50800

uncertainties

Transparent calculations with uncertainties on the quantities involved (aka "error propagation"); calculation of derivatives.

Language:PythonNOASSERTION56800

sequence_braiding

Language:JavaScript1500

genomics

Sphinx documentation source for a computational genomics tutorial.

Language:HTMLMIT3000

sweetviz

Visualize and compare datasets, target values and associations, with one line of code.

Language:PythonMIT287100

ComplexHeatmap

Make Complex Heatmaps

Language:RNOASSERTION126700

empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis

Language:JavaScriptBSD-3-Clause4500

tutorials

Tutorials on phylogenetic and phylogenomic inference

Language:HTML34100

bifrost

Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs

Language:C++BSD-2-Clause19900

CompareM

A toolbox for comparative genomics.

Language:PythonGPL-3.09200

RefineM

A toolbox for improving metagenome-assembled genomes.

Language:PythonGPL-3.06300

biolib

Python package for common tasks in bioinformatic.

Language:PythonGPL-3.01300

PanACoTA

PANgenome with Annotations, COre identification, Tree and corresponding Alignments

Language:PythonAGPL-3.06700

Mash

Fast genome and metagenome distance estimation using MinHash

Language:C++NOASSERTION38100

Unicycler

hybrid assembly pipeline for bacterial genomes

Language:C++GPL-3.053700

referenceseeker

Rapid determination of appropriate reference genomes.

Language:PythonGPL-3.08600

sra-tools

SRA Tools

Language:CNOASSERTION108100

biosample-analysis

analysis of biosamples in INSDC

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zotero-mdnotes

A Zotero plugin to export item metadata and notes as markdown files

Language:JavaScriptGPL-3.0131600

redbiom

Sample search by metadata and features

Language:PythonNOASSERTION4400

bactopia

A flexible pipeline for complete analysis of bacterial genomes

Language:NextflowMIT38200

penrose

Create beautiful diagrams just by typing notation in plain text.

Language:TypeScriptMIT673300

bionitio

Demonstrating best practices for bioinformatics command line tools

Language:ShellMIT11500

knetmaps.js

KnetMaps: a BioJS component to visualize biological knowledge networks

Language:JavaScriptMIT1000

genomesignals

A collection of types of genomic signals different people plot

200

oddgenes

A small database of weird gene annotations

Language:Perl19800

CAT_pack

CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes

Language:PythonMIT17200