eukaryotes

There are 0 repository under eukaryotes topic.

• soedinglab / metaeuk

  MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

  metagenomicseukaryotesgene-predictiongene-discoverybioinformatics
  Language:C 171

• pr2database / pr2database

  Protist Ribosomal Reference database (PR2) - SSU rRNA gene database

  rrnadatabaseeukaryotesmetabarcodingtaxonomy18s-rrna
  Language:R 76

• ibe-uw / tiara

  tiara – a tool for DNA sequence classification

  bioinformaticsclassificationeukaryotesmachine-learningmetagenomicsorganelle
  Language:Python 50

• EngqvistLab / Tome

  A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

  microbiologytemperature-dataenzymesmachine-learningbioinformaticsbacteriaarchaeaeukaryotes
  Language:Python 48

• chmccarthy / Pangloss

  Pangenome analysis of eukaryotes.

  pangenomebioinformaticseukaryotes
  Language:Perl 17

• RogerLab / Eukfinder

  Eukfinder: A pipeline to retrieve microbial eukaryote genomes from metagenomic sequencing data

  bioinformaticsclassificationeukaryotesmetagenomics
  Language:Python 13

• nf-core / metatdenovo

  Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

  nf-corenextflowpipelineworkfloweukaryotesmetagenomicsmetatranscriptomicsprokaryotesviruses
  Language:Nextflow 12

• galikbence / genome_annotation

  Pipeline for eukaryotic genome annotation based on external evidences

  genome-annotationbioinformatics-analysiseukaryotes
  Language:R 8

• pr2database / pr2-primers

  Scripts for paper Vaulot et al. 2022

  database18s-rrnaprimerseukaryotestaxonomymetabarcoding
  Language:R 5

• vmikk / NextITS

  A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio

  eukaryotesfungiitsmetabarcodingnextflowpacbiointernal-transcribed-spacerpipeline
  Language:Nextflow 5

• LucaPizzagalli / motion-microswimmers-simulation

  Simulation of the motion of the eukariotic cell Chlamydomonas Reinhardtii

  simulationphysicsphysics-simulationstochastic-differential-equationssdleukaryotesmicroswimmersde
  Language:C++ 4

• wrf / genome-size

  examination of genome size across all kingdoms

  genomicsgenomeprokaryoteseukaryotescvalue
  Language:R 4

• amsesk / SCGid

  SCGid, a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries

  bioinformatics-pipelinebioinformatics-algorithmsbioinformatics-toolbioinformaticsfungieukaryotessingle-cell-genomicsgenome-assembly-evaluationpython3
  Language:Python 3

• EngqvistLab / orgtools

  A library to get information on organisms and UniProt identifiers. This includes growth temperature, growth ph, pfam domains, taxonomic lineage.

  taxonomic-identifierstaxonomic-lineagesphylogeneticsbioinformaticsmicrobiologybacteriaarchaeaeukaryotes
  Language:Python 2

• sabahzero / Puerto-Nuevo_Coastal-Microbial-Ecology_16S-18S-Workflow_UlHasan-etal

  This is a microbial amplicon sequence (16S and 18S iTag) data and analyses pipeline corresponding to the manuscript, "Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California" for public benefit and usage.

  microbiologysequencecoastalecosystembacteriaarchaeaeukaryotesstatisticspermanovaanovataxonomyamplicon
  2

• balazshorvathreal / MegaVir

  MegaVir is a bioinformatic pipeline for virome characterization and genome assembly.

  amino-acidsbacteriaeukaryotesmetagenomic-pipelinenucleotidesvirus
  Language:R 1

• jcvi-plant-genomics / eucap

  EuCAP, a Eukaryotic Community Annotation Package (adapted from the implementation developed for the Rice Genome Annotation Project)

  eukaryotescommunity-annotationperl-cgimysqlmedicagoarchive
  Language:Perl 1

• ToshkaDev / Motif

  V. M. Gumerov, E. P. Andrianova, M. A. Matilla, Karen M. Page, Elizabet Monteagudo-Cascales, A. C. Dolphin, T. Krell, I. B. Zhulin (2022). Amino acid sensor conserved from bacteria to humans.

  bioinformaticsarchaeabacteriaeukaryotesmolecular-evolutionmotifreceptortree-of-life
  Language:Python 1

• andrewd789 / DNA_extraction_PCR_impacts

  Sequence processing and analysis code used to investigate the effects of different DNA extraction methods and PCR variability on multi-taxon DNA meta-barcoding estimates of soil biodiversity.

  biodiversitydna-extractiondna-metabarcodingeukaryotespcrprokaryotes
  Language:R 0

• cmlglvz / datasets

  Datasets and statistics code used for "Objective 1" for PhD Thesis

  bioinformaticsmicrobiologyecologycoastalpollutionoceans18s-rrnapicophytoplanktoniceukaryotesppepicoeukaryoteschilemicroecology
  Language:HTML 0

• Next-ITS / next-its.github.io

  NextITS pipeline documentation

  eukaryotesfungiinternal-transcribed-spaceritsmetabarcodingpacbio
  0

• SpanishCat / Synyin-Deed

  A program that uses the Synteny Index algorithm to compare between Eukaryotes.

  sisynteny-indexbioinformaticseukaryotesgeneticssequence-alignmentyeastyeast-species
  Language:Perl 0