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PhyloNext: a pipeline for phylogenetic diversity analysis of GBIF-mediated data
BackgroundUnderstanding biodiversity patterns is a central topic in biogeography and ecology, and it is essential for conservation planning and...
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IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods
BackgroundIntegration site (IS) analysis is a fundamental analytical platform for evaluating the safety and efficacy of viral vector based...
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EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets
BackgroundGenome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still...
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scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis
BackgroundHere we present scSNPdemux, a sample demultiplexing pipeline for single-cell RNA sequencing data using natural genetic variations in...
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A pangenome analysis pipeline provides insights into functional gene identification in rice
BackgroundA pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single...
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Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing
Among molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed...
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Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP)
BackgroundTranscriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have...
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Optimizing Variant Calling for Human Genome Analysis: A Comprehensive Pipeline Approach
The identification of genetic variations in large cohorts is a critical issue to identify patient cohorts, disease risks, and to develop more...
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FIOLA: an accelerated pipeline for fluorescence imaging online analysis
Optical microscopy methods such as calcium and voltage imaging enable fast activity readout of large neuronal populations using light. However, the...
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Develo** a bioinformatics pipeline for comparative protein classification analysis
BackgroundProtein classification is a task of paramount importance in various fields of biology. Despite the great momentum of modern implementation...
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transcAnalysis: A Snakemake Pipeline for Differential Expression and Post-transcriptional Modification Analysis
The transcAnalysis pipeline is a comprehensive tool that allows the analysis of transcriptome data. The pipeline allows for analysis of differential...
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DVT: a high-throughput analysis pipeline for locomotion and social behavior in adult Drosophila melanogaster
BackgroundDrosophila melanogaster is excellent animal model for understanding the molecular basis of human neurological and motor disorders. The...
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UMGAP: the Unipept MetaGenomics Analysis Pipeline
BackgroundShotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep...
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PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data
BackgroundPopulation structure and cryptic relatedness between individuals (samples) are two major factors affecting false positives in genome-wide...
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ShapeMetrics: A 3D Cell Segmentation Pipeline for Single-Cell Spatial Morphometric Analysis
There is a growing need for single-cell level data analysis in correlation with the advancements of microscopy techniques. Morphology-based...
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Data Analysis Pipeline for scRNA-seq Experiments to Study Early Oogenesis
Germ cells as the means for the transmission of genetic information between generations have been a hot topic of research for decades. The analysis...
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Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance
BackgroundThe advent of single-cell RNA-sequencing (scRNA-seq) has driven significant computational methods development for all steps in the...
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Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis
Single-cell multiomic analysis of the epigenome, transcriptome, and proteome allows for comprehensive characterization of the molecular circuitry...
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Open-source analytical pipeline for robust data analysis, visualizations and sharing in crop breeding
BackgroundDevelo** a systematic phenotypic data analysis pipeline, creating enhanced visualizations, and interpreting the results is crucial to...
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msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data
BackgroundDNA methylation is an important epigenetic modification that is known to regulate gene expression. Whole-genome bisulfite sequencing (WGBS)...
