jun305

jun305's Stars

• Arkadiy-Garber/FeGenie

  HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes

  Language:Python5411

• hbucqp/ResBlaster

  find antimicrobial resistance/ virulence genes in assembled genomes

  Language:Python6

• ChiLiubio/microeco

  An R package for data analysis in microbial community ecology

  Language:R19156

• CharlesHahn/DuIvyTools

  A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).

  Language:Python5510

• tubiana/protocolGromacs

  Automatic gromacs protocol from preparation to production with ligand parametrization through

  Language:Shell5614

• Valdes-Tresanco-MS/AMDock

  (Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina

  Language:Python5816

• isabelschober/proteinortho_curves

  Draw pan- and core-genome curves from proteinortho output

  Language:R7

• schneebergerlab/plotsr

  Tool to plot synteny and structural rearrangements between genomes

  Language:Python27427

• schneebergerlab/syri

  Synteny and Rearrangement Identifier

  Language:Cython31236

• arpcard/rgi

  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

  Language:Python31976

• phac-nml/staramr

  Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

  Language:Python11526

• YaoLab-Bioinfo/shinyCircos

  an R/shiny application for creation of Circos plot interactively

  Language:HTML15147

• griffithlab/rnaseq_tutorial

  Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

  Language:R1.3k617

• apredeus/multi-bacpipe

  A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments

  Language:Perl102

• Frahiriart/prokfold

  RNA-seq pipeline for prokaryote

  Language:Python1

• PoeticPremium6/RNA-SEQ--Raw-reads-to-Counts

  A variety of RNA-Seq pipelines are presented: Tuxedo for bacteria, Tuxedo for Humans, and HISAT2 for Humans. Additionally, you can find scripts for normalization of RNA-Seq Counts and scripts for visualization of DEGs

  Language:R11

• gxcuizy/Python

  Python3编写的各种大小程序，包含从零学Python系列、12306抢票、省市区地址库以及系列网站爬虫等学习源码

  Language:Python3.7k1.3k

• lh3/bioawk

  BWK awk modified for biological data

  Language:C590121

• marekborowiec/AMAS

  Calculate summary statistics and manipulate multiple sequence alignments

  Language:Python7214

• ChrisCreevey/catsequences

  A tool for concatenating multiple fasta alignments for supermatrix phylogenetic analyses

  Language:C196

• jvollme/PO_2_MLSA

  Enables the calculation of phylogenies based on single copy core genome gene products, based on bidirectional BLAST results obtained with proteinortho

  Language:Python4

• aleimba/bac-genomics-scripts

  Collection of scripts for bacterial genomics

  Language:Perl4233

• metagenlab/locus2genoplotr

  Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram

  Language:Python101

• moshi4/pyGenomeViz

  A genome visualization python package for comparative genomics

  Language:Python26221

• thackl/gggenomes

  A grammar of graphics for comparative genomics

  Language:R58064

• wilkox/gggenes

  ➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

  Language:R48649

• medema-group/BiG-SCAPE

  Similarity networks of biosynthetic gene clusters

  Language:JavaScript6125

• nuzla/Pangenome-Graphs-Workshop

  This repository contains material to construct pangenome graphs for a small bacteria dataset detailing every step in the Nesi environment.

  Language:HTML2

• alipirani88/snpkit

  Modular workflow for Microbial Variant Calling and SNP diagnostics.

  Language:Python54

• lmc297/SNPBac

  SNP and variant calling pipeline for bacteria

  76