Alternatives and similar repositories for speedyseq

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

• ggloor / CoDaSeq
  Functions for compositional analysis of high throughput sequencing
  ☆29Updated last year
• schuyler-smith / phylosmith
  functions for analyzing phyloseq data
  ☆27Updated 4 months ago
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆51Updated 3 years ago
• statdivlab / radEmu
  ☆55Updated last week
• vmikk / metagMisc
  Miscellaneous functions for metagenomic analysis.
  ☆50Updated last week
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• microsud / microbiomeutilities
  The is mostly a wrapper tool using phyloseq and microbiome R packages.
  ☆34Updated 2 years ago
• SchlossLab / schtools
  Schloss Lab Tools for Reproducible Microbiome Research 💩
  ☆31Updated last year
• brendankelly / micropower
  power estimation for microbiome studies analyzed with pairwise distances and PERMANOVA
  ☆37Updated 9 years ago
• mahendra-mariadassou / phyloseq-extended
  Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…
  ☆33Updated 3 months ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆33Updated 4 years ago
• nextgenusfs / amptk
  AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
  ☆38Updated last year
• knightlab-analyses / reference-frames
  ☆20Updated 4 years ago
• zoecastillo / microbiomeExplorer
  The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…
  ☆71Updated 2 years ago
• shandley / Microbiome-Analysis-Using-R
  Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.
  ☆27Updated 2 years ago
• ChiLiubio / file2meco
  Transform files to the microtable object with microeco package
  ☆27Updated 2 months ago
• yhwu / idemp
  Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files
  ☆31Updated 7 years ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 4 months ago
• nhanhocu / metamicrobiomeR
  An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studi…
  ☆33Updated 4 years ago
• vmaffei / dada2_to_picrust
  Experimental pipeline to perform de novo PICRUSt on de-noised amplicon sequence variants (ASV)
  ☆19Updated 6 years ago
• frederic-mahe / swarm
  A robust and fast clustering method for amplicon-based studies
  ☆31Updated 2 years ago
• vallenderlab / MicrobiomeR
  A comprehensive and customizable R package for microbiome analysis.
  ☆23Updated this week
• gmteunisse / fantaxtic
  Fantaxtic - Nested Bar Plots for Phyloseq Data
  ☆30Updated 10 months ago
• jlw-ecoevo / gRodon
  ☆17Updated 2 years ago
• MadsAlbertsen / ampvis
  [deprecated] Please use ampvis2
  ☆8Updated 7 years ago
• arendsee / rhmmer
  Simple R utilities for working with HMMER
  ☆20Updated 8 months ago
• OSS-Lab / MetQy
  Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247936/)
  ☆18Updated 3 years ago
• KasperSkytte / ampvis2
  Tools for visualising microbial community amplicon data
  ☆67Updated last month
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆54Updated 3 years ago
• adw96 / DivNet
  diversity estimation under ecological networks
  ☆83Updated last month