Topic: "metatranscriptomics"
merenlab/anvio
An analysis and visualization platform for 'omics data
Language: Python - Size: 745 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 468 - Forks: 148
sortmerna/sortmerna
SortMeRNA: next-generation sequence filtering and alignment tool
Language: C++ - Size: 88.9 MB - Last synced at: 30 days ago - Pushed at: 5 months ago - Stars: 259 - Forks: 68
soedinglab/plass
sensitive and precise assembly of short sequencing reads
Language: C - Size: 27.1 MB - Last synced at: about 23 hours ago - Pushed at: 7 months ago - Stars: 155 - Forks: 15
jolespin/veba
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
Language: Python - Size: 55 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 84 - Forks: 11
iquasere/KEGGCharter
A tool for representing genomic potential and transcriptomic expression into KEGG pathways
Language: Python - Size: 519 MB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 54 - Forks: 7
iquasere/MOSCA
Meta-Omics Software for Community Analysis
Language: Python - Size: 441 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 35 - Forks: 4
nf-core/metatdenovo
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
Language: Nextflow - Size: 103 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 30 - Forks: 14
ablab/metaGT
Pipeline for metagenome and metatranscriptome joint assembly
Language: Nextflow - Size: 1.96 MB - Last synced at: 12 months ago - Pushed at: about 2 years ago - Stars: 15 - Forks: 0
FEI38750/MTD
MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
Language: R - Size: 23.7 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 14 - Forks: 7
ASaiM/framework
Open-source opinionated Galaxy-based framework for microbiota analysis
Language: HTML - Size: 39.7 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 13 - Forks: 7
KevinMcDonnell6/chordomics
Interactive visualisation and data annotation for meta-omics data
Language: R - Size: 69.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 4
PNNL-CompBio/perseq
:cake: Per sequence functional classification and taxonomic assignments
Language: HTML - Size: 69.7 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 7 - Forks: 0
NBISweden/contigtax
Taxonomic classification of metagenomic contigs
Language: Python - Size: 4.26 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 6 - Forks: 6
anwarMZ/CoMW
Comparative Metatranscriptomics Workflow
Language: Python - Size: 175 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 6 - Forks: 3
OpenOmics/metamorph
Metagenomics and Metatranscriptomics pipeline
Language: Python - Size: 782 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 5 - Forks: 1
muzafferarikan/gNOMO2
gNOMO2 allows integrated multi-omics analyses of microbiomes
Language: Python - Size: 1.32 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 5 - Forks: 1
icaromsc/nf-core-phiflow
Language: Nextflow - Size: 2.26 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 0
microbiomedata/metaT
Metatranscriptomics workflow
Language: WDL - Size: 22.2 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 4 - Forks: 2
BirgitRijvers/EMC-MetaMicrobes
Nextflow pipeline to detect and classify microbial reads in sequencing data from human samples.
Language: Nextflow - Size: 10.4 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 4 - Forks: 2
poursalavati/SOVAP
The Soil Virome Analysis Pipeline (SOVAP) is designed to process, analyze, and annotate viromics and metagenomics data using cutting-edge tools, providing valuable insights into the virome and microbial communities found in complex environments, such as soil ecosystems.
Language: Python - Size: 191 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 1
SchlossLab/Jenior_Metatranscriptomics_mSphere_2018
Repository associated with Jenior ML, et al. (2018). mSphere.
Language: R - Size: 261 MB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 4 - Forks: 2
SilentGene/MultiOmicAnalysis
Genome-centric Multi-omic Analysis Workflow for the Marinimicrobia paper
Language: Shell - Size: 27.3 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 3
raw-lab/metaome_stats
Statistical package for metaome denovo assembly results.
Language: Python - Size: 2.64 MB - Last synced at: 9 months ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 16
rjstevick/NBayTNCoystersAnalysis
Scripts for analysis of metatranscriptomic and 16S rRNA amplicon data from wild oysters in Narragansett Bay
Language: R - Size: 21.8 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1
AU-ENVS-Bioinformatics/TotalRNA-Snakemake
A pipeline for TotalRNA analysis
Language: Jupyter Notebook - Size: 539 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1
erikrikarddaniel/magmap
Nextflow (nf-core) workflow for mapping reads to large collections of genomes.
Language: Nextflow - Size: 2.26 MB - Last synced at: 10 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1
gabrielvpina/viralquest
A pipeline for viral diversity analysis
Language: Python - Size: 89.3 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0
judithguitart/Multi-omics-analysis
Multi-omics analysis of swine gut microbiome after different treatments for post-weaning diarrhoea in a longitudinal study
Size: 6.83 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 0 - Forks: 0
biocoms/biocoms.github.io
Laboratory website
Language: HTML - Size: 3.85 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
gabrielvpina/ViewVir
ViewVir - A pipeline for viral diversity analysis
Language: Python - Size: 14.4 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
hiraokas/ProbeCaptureEnrichmentSequencing_amoA
Probe capture enrichment sequencing of amoA genes
Language: Shell - Size: 3.11 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
hermidalc/dragonfish
A fast, efficient, and accurate functional and taxonomic meta-omic profiler built on Pufferfish and the ccdBG
Language: Python - Size: 9.28 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
rjstevick/PJnitrogenOysterMicrobiomes
Study of farmed oysters and nitrogen cycling in Point Judith Pond, RI. Scripts for analysis of 16S rRNA amplicon and metatranscriptomic data.
Language: HTML - Size: 31 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
N-Heck-1/Microeukaryotic-predators-shape-the-wastewater-microbiome
Language: Shell - Size: 3.42 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
jmpolinski/Moytirra-Hydrothermal-Vent-Plume
A primary goal of this research was to characterize vent plume biogeography across a spatial gradient. This study was done in collaboration with OceanX during the 2021 Young Explorers Program.
Language: R - Size: 54.8 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
WEHI-ResearchComputing/samsa2-nf
Nextflow translation for SAMSA2 metatranscriptomics pipeline. Tailored for running on WEHI Milton.
Language: Python - Size: 48.8 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
MiriamMarinS/NibenMetaTranscriptomics
Meta Transcriptomic study of Nicotiana benthamiana to look for high expressed locations in the genome.
Language: Jupyter Notebook - Size: 1.5 MB - Last synced at: 4 months ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
metavannier/metatranscriptomics-bulkrnaseq_workflow
This workflow performs a metatranscriptomics and bulk RNAseq analysis from the sequencing output data to the differential expression analyses.
Language: Python - Size: 91.8 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 2
genomeud/SRA-ome
Code for systematically classify data in SRA according to all the taxa present in the reads (SRA-metagenome)
Language: C++ - Size: 461 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
dombraccia/H2S
Code bank for analysis performed in the manuscript" "The capacity to produce hydrogen sulfide (H2S) via cysteine degradation is ubiquitous in the human gut microbiome"
Language: R - Size: 119 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
