bioinformatics-tool

There are 447 repositories under bioinformatics-tool topic.

  • tseemann/abricate

    :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

    Language:Perl3972820495
  • lightdock

    lightdock/lightdock

    Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

    Language:Python328127245

  • sunduanchen/Scissor

    Scissor package

    Language:C++21336735

  • inab/trimal

    A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

    Language:C++199127245
  • RNAlysis

    GuyTeichman/RNAlysis

    Analyze your RNA sequencing data without writing a single line of code

    Language:Python13143213

  • KarchinLab/open-cravat

    A modular annotation tool for genomic variants

    Language:JavaScript1182022731

  • avrabyt/YouTube-Tutorials

    📹 Collection of my Youtube Tutorials over the years! Read, write, and share what you create ✨🎈

    Language:Python1176348
  • seqfu2

    telatin/seqfu2

    :rocket: seqfu - Sequece Fastx Utilities

    Language:Nim1143209

  • Superzchen/iLearnPlus

    iLearnPlus is the first machine-learning platform with both graphical- and web-based user interface that enables the construction of automated machine-learning pipelines for computational analysis and predictions using nucleic acid and protein sequences.

    Language:Python10641433

  • bcgsc/RNA-Bloom

    :hibiscus: reference-free transcriptome assembly for short and long reads

    Language:Java10311697
  • BioBlender21

    PabloEnmanuelRamos/BioBlender21

    Blender plugin to process biological data and molecular work.

    Language:Python86141412

  • imgag/ClinCNV

    Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

    Language:R8310474

  • chriscainx/mnnpy

    An implementation of MNN (Mutual Nearest Neighbors) correct in python.

    Language:Python7354632

  • josiahseaman/FluentDNA

    FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

    Language:JavaScript657827

  • ShujiaHuang/geneview

    Genomics data visualization in Python by using matplotlib.

    Language:Python65538

  • JetBrains-Research/snakecharm

    Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

    Language:Python6154207

  • rcedgar/reseek

    Protein structure alignment and search algorithm

    Language:C++592113

  • bcgsc/tigmint

    ⛓ Correct misassemblies using linked AND long reads

    Language:Python58175313

  • muellan/metacache

    memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

    Language:C++5874313

  • ebi-jdispatcher/webservice-clients

    A collection of Web Service Clients to consume EBI's Job Dispatcher tools via REST APIs

    Language:Perl524523

  • ncsa/NEAT

    NEAT (NExt-generation Analysis Toolkit) simulates next-gen sequencing reads and can learn simulation parameters from real data.

    Language:Python5257715

  • bobeobibo/phigaro

    Phigaro is a scalable command-line tool for predicting phages and prophages

    Language:HTML5143515
  • stitchr

    JamieHeather/stitchr

    Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info

    Language:Python5133610

  • onclave/NSGA-II

    an implementation of NSGA-II in java

    Language:Java4921423
  • HTStream

    s4hts/HTStream

    A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes

    Language:C++49813310

  • clemgoub/TE-Aid

    Annotation helper tool for the manual curation of transposable element consensus sequences

    Language:R47288

  • treangenlab/methphaser

    MethPhaser: methylation-based haplotype phasing of human genomes

    Language:Python463171

  • YaqiangCao/cLoops2

    Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.

    Language:Python451148

  • telatin/covtobed

    ⛰ covtobed | Convert the coverage track from a BAM file into a BED file

    Language:C++431123

  • labstructbioinf/localpdb

    Python package to manage protein structures and their annotations

    Language:Python420195

  • biologger/speciesprimer

    The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.

    Language:Python4133219

  • bcgsc/goldrush

    Linear-time de novo Long Read Assembler

    Language:C++3910452

  • akcorut/kGWASflow

    kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

    Language:Python382359

  • Kukuster/SumStatsRehab

    GWAS summary statistics files QC tool

    Language:Python38276

  • genotoul-bioinfo/Binette

    A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.

    Language:Python333200

  • Superzchen/iFeatureOmega-CLI

    iFeatureOmega is a comprehensive platform for generating, analyzing and visualizing more than 170 representations for biological sequences, 3D structures and ligands. To the best of our knowledge, iFeatureOmega supplies the largest number of feature extraction and analysis approaches for most molecule types compared to other pipelines. Three versions (i.e. iFeatureOmega-Web, iFeatureOmega-GUI and iFeatureOmega-CLI) of iFeatureOmega have been made available to cater to both experienced bioinformaticians and biologists with limited programming expertise. iFeatureOmega also expands its functionality by integrating 15 feature analysis algorithms (including ten cluster algorithms, three dimensionality reduction algorithms and two feature normalization algorithms) and providing nine types of interactive plots for statistical features visualization (including histogram, kernel density plot, heatmap, boxplot, line chart, scatter plot, circular plot, protein three dimensional structure plot and ligand structure plot). iFeatureOmega is an open-source platform for academic purposes. The web server can be accessed through http://ifeature2.erc.monash.edu and the GUI and CLI versions can be download at: https://github.com/Superzchen/iFeatureOmega-GUI and https://github.com/Superzchen/iFeatureOmega-CLI, respectively.

    Language:Python322210