Topic 165

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53 items. Top items listed below.

SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities 165 62 13 7 4

CandiHap: a toolkit for haplotype analysis for sequence of samples and fast identification of candidate causal gene(s) in genome-wide association study 165 13 4

TBtools - an integrative toolkit developed for interactive analyses of big biological data 165 62 13 4

SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat 165 62 13 4

ATAV: a comprehensive platform for population-scale genomic analyses 165 62 13 4

DBSCAN-SWA: an integrated tool for rapid prophage detection and annotation 165 13 4

Conditional Analysis Cakewalk 165 13 4

AmpliconDesign - An interactive web server for the design of high-throughput targeted DNA methylation assays 165 13 4

Ares-GT: design of guide RNAs targeting multiple genes for CRISPR-Cas experiments 165 13 4

A decoupled, modular and scriptable architecture for tools to curate data platforms 165 13 4

New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics 165 13 4

ClassifyCNV: a tool for clinical annotation of copy-number variants 165 13 4

HAPPI GWAS: Holistic Analysis with Pre and Post Integration GWAS 165 13 4

EdiTyper: a high-throughput tool for analysis of targeted sequencing data from genome editing experiments 165 13 4

RAD: a web application to identify region associated differentially expressed genes 165 62 31 13 4

piRPheno: a manually curated database to prioritize and analyze human disease related piRNAs 165 62 13 4

FAN-C: A Feature-rich Framework for the Analysis and Visualisation of C data 165 13 4

unCOVERApp: an interactive graphical application for clinical assessment of sequence coverage at the base-pair level 165 62 13 4

CancerVar: a web server for improved evidence-based clinical interpretation of cancer somatic mutations and copy number abnormalities 165 13 4

Effective variant filtering and expected candidate variant yield in studies of rare human disease 165 97 13 4

AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data 13 4

CRISPRCasTyper: An automated tool for the identification, annotation and classification of CRISPR-Cas loci 165 13 4

A method to map and interpret pleiotropic loci using summary statistics of multiple traits 165 13 4

RatsPub: a webservice aided by deep learning to mine PubMed for addiction-related genes 165 62 13 4

ipcoal: An interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network 165 13 4

Multi-omics Visualization Platform: An extensible Galaxy plug-In for multi-omics data visualization and exploration 165 62 45 4

CoffeeProt: An online tool for correlation and functional enrichment of proteome-wide systems genetics 165 62 13 4

HamHeat: A fast and simple package for calculating Hamming distance from multiple sequence data for heatmap visualization 165 13 4

Dix-seq: An integrated pipeline for fast amplicon data analysis 13 4

Pangaea: A modular and extensible collection of tools for mining context dependent gene relationships from the biomedical literature 165 13 4

Rcirc: an R package for circRNA analyses and visualization 13 4

cognac: rapid generation of concatenated gene alignments for phylogenetic inferencefrom large whole genome sequencing datasets 13 4

Haplocheck: Phylogeny-based Contamination Detection in Mitochondrial and Whole-Genome Sequencing Studies 13 4

ErrorX: automated error correction for immune repertoire sequencing datasets 165 13 4

VarFish - Collaborative and Comprehensive Variant Analysis for Diagnosis and Research 165 62 4

VarStack: a Web Tool for Data Retrieval to Interpret Somatic Variants in Cancer 165 62 13 4

SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts 165 62 13 4

ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data 176 62 4

IMIX: A multivariate mixture model approach to integrative analysis of multiple types of omics data 165 13 4

SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets 165 162 13 4

ProkSeq for complete analysis of RNA-seq data from prokaryotes 13 4

MetaPhat: Detecting and decomposing multivariate associations from univariate genome-wide association statistics 165 19 13 4

Bashing irreproducibility with shournal 165 13 4

Corna - An Open Source Python Tool For Natural Abundance Correction In Isotope Tracer Experiments 62 13 4

The Gene Expression Deconvolution Interactive Tool (GEDIT): Accurate Cell Type Quantification from Gene Expression Data 13 4

miRSwitch: Detecting microRNA arm shift and switch events 165 62 13 4

DrawAlignR: An interactive tool for across run chromatogram alignment visualization 13 4

Multi Locus View: An Extensible Web Based Tool for the Analysis of Genomic Data 13 4

gwaRs: an R shiny web application for visualizing genome-wide association studies data 13 4

NoRCE: Non-coding RNA Sets Cis Enrichment Tool 13 4

mutyper: assigning and summarizing mutation types for analyzing germline mutation spectra 13 4

SMN1 copy-number and sequence variant analysis from next generation sequencing data 165 13 4

CIAlign - A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments. 165 62 4

TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data 62 13 4

NeuroPycon: An open-source Python toolbox for fast multi-modal and reproducible brain connectivity pipelines 62 13 4

CoV-Seq: SARS-CoV-2 Genome Analysis and Visualization 13 4

Advanced Research Infrastructure for Experimentation in genomicS (ARIES): a lustrum of Galaxy experience 165 62 4

cmvdrg - An R package for Human Cytomegalovirus antiviral Drug Resistance Genotyping 13 4

SambaR: an R package for fast, easy and reproducible population-genetic analyses of biallelic SNP datasets 62 13 4

BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data. 13 4

MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations 13 4

CoMut: Visualizing integrated molecular information with comutation plots 13 4

animalcules: Interactive Microbiome Analytics 1 and Visualization in R 13 4

ZEAMAP, a comprehensive database adapted to the maize multi-omics era 165 62 53 4

CHOmics: a web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines 62 13 4

DamageProfiler: Fast damage pattern calculation for ancient DNA 176 62 4

MultiPhATE2: Code for Functional Annotation and Comparison of Bacteriophage Genomes 13 4

Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis 13 4

Bactopia: a flexible pipeline for complete analysis of bacterial genomes 13 4

MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection 13 4

Bibliome Variant Database: Automated Identification and Annotation of Genetic Variants in Primary Literature 165 97 62 4

MicrobeAnnotator: a user-friendly, comprehensive microbial genome annotation pipeline 13 4

ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes 13 7 4

idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates 13 4

PanGIA: A Metagenomics Analytical Framework for RoutineBiosurveillance and Clinical Pathogen Detection 13 4

metabolisHMM: Phylogenomic analysis for exploration of microbial phylogenies and metabolic pathways 13 4

MapCaller - An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data 13 4

Broccoli: combining phylogenetic and network analyses for orthology assignment 13 4

Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation 176 165 62 4

Platon: identification and characterization of bacterial plasmid contigs in short-read draft assembliesexploiting protein-sequence-based replicon distribution scores 13 4

ADMIXPIPE: Population analyses in ADMIXTURE for non-model organisms 184 13 4

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data 13 4

ideal: an R/Bioconductor package for Interactive Differential Expression Analysis 62 13 4

Balrog: A universal protein model for prokaryotic gene prediction 162 13 4

Efficient and Flexible Integration of Variant Characteristics in Rare Variant Association Studies Using Integrated Nested Laplace Approximation 145 13 4

circHiC: circular visualization of Hi-C data and integration of genomic data 165 13 4

figureComposer: A web-based interactive multi-panel bio- infographic designing tool 13 4

FEATS: Feature selection based clustering of single-cell RNA-seq data 147 13 4

fsbrain: an R package for the visualization ofstructural neuroimaging data 165 13 4

Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data 165 13 4

PFRED: A computational platform for siRNA and antisense oligonucleotides design. 13 4

coronapp: a Web Application to Annotate and Monitor SARS-CoV-2 Mutations 13 4

MetaFunc: Taxonomic and Functional Analyses of High Throughput Sequencing for Microbiomes 13 4

rearrvisr: an R package to detect, classify, and visualize genome rearrangements 13 4

dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology 13 4

GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline 13 4

Shiny-SoSV: A web-based performance calculator for somatic structural variant detection 62 13 4

Cuttlefish: Fast, parallel, and low-memory compaction of de Bruijn graphs from large-scale genome collections 162 13 4

FlexDotPlot: a universal and modular dot plot visualization tool for complex multifaceted data 13 4

Liftoff: an accurate gene annotation mapping tool 13 4