Alternatives and similar repositories for plasmapR

Users that are interested in plasmapR are comparing it to the libraries listed below

• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 3 months ago
• nvelden / geneviewer
  An R package designed for drawing gene arrow maps
  ☆90Updated last week
• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆77Updated 2 months ago
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆65Updated last year
• victoriapascal / gutsmash
  gutSMASH
  ☆55Updated last week
• zoecastillo / microbiomeExplorer
  The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…
  ☆72Updated 3 years ago
• Wytamma / GISAIDR
  Programmatically interact with the GISAID database.
  ☆78Updated 2 months ago
• thomazbastiaanssen / Tjazi
  A microbiome analysis toolkit for R
  ☆24Updated 2 years ago
• microsud / dysbiosisR
  The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures
  ☆15Updated 2 years ago
• FrederickHuangLin / ANCOM-Code-Archive
  Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM…
  ☆62Updated 3 years ago
• drostlab / orthologr
  Genome wide orthology inference and dNdS estimation
  ☆96Updated last month
• nf-core / funcscan
  (Meta-)genome screening for functional and natural product gene sequences
  ☆92Updated last week
• KasperSkytte / ampvis2
  Tools for visualising microbial community amplicon data
  ☆69Updated last month
• AstrobioMike / bit
  Bioinformatics Tools
  ☆90Updated last week
• wejlab / animalcules
  R shiny app for interactive microbiome analysis
  ☆56Updated 4 months ago
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• ohmeta / metapi
  A general metagenomics data mining system focus on robust microbiome research
  ☆58Updated last year
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆21Updated 2 years ago
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 9 months ago
• arendsee / rhmmer
  Simple R utilities for working with HMMER
  ☆20Updated last year
• biobakery / maaslin3
  MaAsLin3: Microbiome Multivariate Association with Linear Models
  ☆47Updated last week
• waldronlab / lefser
  R implementation of the LEfSe method
  ☆59Updated 5 months ago
• mikemc / speedyseq
  Speedy versions of phyloseq functions
  ☆48Updated last year
• GraceYoon / SPRING
  Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data
  ☆24Updated 3 years ago
• microbiome / OMA
  Orchestrating Microbiome Analysis
  ☆104Updated this week
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆69Updated last month
• metageni / SUPER-FOCUS
  A tool for agile functional analysis of shotgun metagenomic data
  ☆25Updated last year
• schuyler-smith / phylosmith
  functions for analyzing phyloseq data
  ☆28Updated 8 months ago
• david-barnett / microViz
  R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
  ☆120Updated 2 months ago
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year