RNA-seq workflow: gene-level exploratory analysis and differential expression
Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified t...940 days ago
847 days ago
GToTree: a user-friendly workflow for phylogenomics
GToTree is a user-friendly workflow for phylogenomics intended to give more researchers the capability to create phylogenomic trees. The open-access Bioinformatics Journal publication is available here, and documentation and examples can be found at the wiki here.803 days ago
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CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
...meta approach, analyzing the predictions of other tools in order to get an improved precision and recall. Please note that the CrowdGO snakemake workflow is currently only tested on U...711 days ago
Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes
Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding gen...ettings to retain high-quality alignments for phylogenetic inference. The workflow produces a detailed report th...75 days ago
pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction
...eline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across mult...75 days ago
CLAW: Chloroplast Long-read Assembly Workflow
CLAW (Chloroplast Long-read Assembly Workflow) is an mostly-automated Snakemake-based workflow for the assembly of chloroplast genomes. CLAW uses chloroplast long-reads, which are baited out of larger read li...75 days ago
bacLIFE: an automated genome mining tool for identification of lifestyle associated genes
bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate...52 days ago