BioInformatix Resources

Bioinformatics Tools Built for Biological Data

Explore open-source applications, pipelines and utilities developed for genomics, transcriptomics, machine learning, structural bioinformatics and biological data processing.

Explore Tools View GitHub
BioInformatix Software Lab
sample.fastqvariants.vcfmodel.pkl
Biological dataAnalyzeResults
$ bioinformatix run workflow [ok] input validated [ok] analysis modules ready

Featured Software

Explore three larger research environments built to support machine learning, structural bioinformatics and cancer data analysis.

ML workspaceReady
AI & Machine LearningDesktop Application

Bioinformatics AutoML Studio

A graphical machine learning environment for gene expression, RNA-Seq and tabular omics datasets.

  • Data preprocessing
  • Classification and clustering
  • PCA and exploratory analysis
  • Feature importance
  • Machine learning workflows
GitHub
Structure viewer3D
Structural BioinformaticsResearch Web Application

ProteinScape

Predict and interactively explore protein 3D structures from amino-acid sequences with ESMFold-related workflows.

  • Protein sequence input
  • Structure prediction workflows
  • Interactive 3D visualization
  • Structure-focused exploration
GitHub Try Live Demo
Cancer data labExplore
Cancer Genomics / AIResearch Application

CRC-DataLab

An exploratory colorectal cancer data platform combining multiple computational analysis approaches.

  • Expression analysis
  • Variant exploration
  • Machine learning
  • Text mining
  • Survival-related analysis
GitHub Try Live Demo

Tool Explorer

Bioinformatics software by workflow

Filter BioInformatix-developed applications, bioinformatics pipelines and Python tools by the type of biological analysis you need.

Filter by category

Showing all 10 tools.

automl_studio.app
AI & Machine Learning

Bioinformatics AutoML Studio

A graphical environment for preprocessing, exploring and applying machine learning to biological datasets.

TypeDesktop Application
StatusOpen Source
Gene expressionRNA-SeqTabular omicsML
GitHub
Technical snapshot
Best suited forExploratory machine learning with biological tables.
InputsGene expression, RNA-Seq and tabular omics data.
OutputsExploratory results, models and feature insights.
MethodsPreprocessing, PCA, classification and clustering.
RepositoryOpen on GitHub
crc_datalab.app
Cancer Genomics / AI

CRC-DataLab

An exploratory platform for colorectal cancer expression, variant, machine learning, text mining and survival-related analysis.

TypeResearch Application
StatusOpen Source
ExpressionVariantsSurvivalText mining
GitHub Try Live Demo
Technical snapshot
Best suited forExploratory colorectal cancer research.
InputsExpression, variant and related cancer datasets.
OutputsExploratory tables, plots and model results.
MethodsExpression analysis, ML, text mining and survival-related analysis.
RepositoryOpen on GitHub
single_cell.explorer
Transcriptomics / Single Cell

Single-Cell RNA-Seq Explorer

An interactive application for exploring single-cell RNA-Seq datasets.

TypeInteractive Application
StatusOpen Source
scRNA-SeqGene expressionInteractive exploration
GitHub
Technical snapshot
Best suited forInteractive single-cell transcriptomics exploration.
InputsSingle-cell RNA-Seq datasets.
OutputsInteractive views and exploratory results.
Data focusCell-level gene expression.
RepositoryOpen on GitHub
sra_fetch_convert.sh
NGS Utility

SRA Fetch & Convert

A utility that simplifies downloading NCBI SRA datasets and converting accession IDs into FASTQ files.

TypeBioinformatics Utility
StatusOpen Source
NCBI SRAAccession IDsFASTQNGS
GitHub
Technical snapshot
Best suited forPreparing public sequencing data for downstream workflows.
InputsNCBI SRA accession IDs.
OutputsFASTQ sequence files.
WorkflowFetch SRA data and convert it to FASTQ.
RepositoryOpen on GitHub
proteinscape.web
Structural Bioinformatics

ProteinScape

A research web application for predicting and interactively viewing protein 3D structures from amino-acid sequences.

TypeResearch Web Application
StatusOpen Source
Protein sequence3D structureESMFold-related
GitHub Try Live Demo
Technical snapshot
Best suited forExploratory protein structure work.
InputsAmino-acid sequences.
OutputsPredicted structures and interactive 3D views.
MethodsESMFold-related structure prediction workflows.
RepositoryOpen on GitHub
bio_wrangler.py
Bioinformatics Data Processing

Bio-Wrangler

Python utilities for loading, filtering, merging and summarizing common biological file formats.

TypePython Package
StatusOpen Source
FASTAFASTQVCFGFFPython
GitHub
Technical snapshot
Best suited forReusable biological file processing in Python.
InputsFASTA, FASTQ, VCF and GFF files.
OutputsFiltered, merged and summarized data.
TechnologyPython package utilities.
RepositoryOpen on GitHub
bioinformatics_gui.app
General Bioinformatics

Bioinformatics GUI Suite

A desktop graphical interface for common bioinformatics analysis tasks.

TypeDesktop GUI Suite
StatusOpen Source
AlignmentVariantsPhylogeneticsAnnotation
GitHub
Technical snapshot
Best suited forGraphical access to common analysis tasks.
InputsTask-dependent biological sequence and annotation data.
OutputsTask-dependent analysis results.
AreasAlignment, variants, phylogenetics and genome annotation.
RepositoryOpen on GitHub
bioarray.explorer
Microarray / Biomarker Analysis

BioArrayExplorer

An interactive application for microarray metadata handling, differential expression and functional analysis.

TypeInteractive Research Application
StatusOpen Source
MicroarrayMetadataDifferential expressionFunctional analysis
GitHub
Technical snapshot
Best suited forExploratory microarray and biomarker analysis.
InputsMicroarray expression data and metadata.
OutputsDifferential expression and functional analysis results.
Data focusMicroarray expression and sample metadata.
RepositoryOpen on GitHub
rnaseq_pipeline.sh
Transcriptomics / NGS

RNA-Seq Data Processing and Analysis Pipeline

An automated command-line workflow for processing RNA-Seq data from raw reads through quality reporting.

TypeCommand-Line Pipeline
StatusOpen Source
FASTQQCTrimmingSTARMultiQC
GitHub
Technical snapshot
Best suited forAutomated RNA-Seq preprocessing and alignment.
InputsFASTQ reads.
OutputsAligned and processed data with quality reports.
StagesQC, trimming, STAR alignment, coverage processing and MultiQC.
RepositoryOpen on GitHub
pulmocheck.streamlit
Applied Machine LearningExperimental

PulmoCheck

An experimental Streamlit application for exploring lung cancer risk factors and predictive models.

TypeStreamlit Research Application
StatusOpen Source Research Tool
StreamlitRisk factorsPredictive modelingApplied ML
GitHub Try Live Demo
Technical snapshot
Best suited forExperimental applied ML exploration.
InputsLung cancer risk-factor data.
OutputsInteractive exploration and predictive-model experiments.
TechnologyStreamlit application.
RepositoryOpen on GitHub

Task Router

What Do You Want to Do?

Start with a bioinformatics task, then jump directly to the software designed for that workflow.

Download sequencing dataSRA Fetch & Convert Process FASTA / FASTQ / VCF / GFFBio-Wrangler Process RNA-Seq dataRNA-Seq Data Processing and Analysis Pipeline Explore single-cell RNA-SeqSingle-Cell RNA-Seq Explorer Analyze microarray dataBioArrayExplorer Run machine learning on biological dataBioinformatics AutoML Studio Predict and explore protein structuresProteinScape Explore colorectal cancer datasetsCRC-DataLab

Open Source

Built Openly

Many BioInformatix tools are available as open-source projects. Explore the source code, test the software, report issues and contribute improvements.

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Related Learning

Learn the Science Behind the Tools

Build the scientific and computational foundations that support these software workflows with related BioInformatix training.

Bioinformatics AutoML Studio

Learn Machine Learning in Bioinformatics: From Theory to Practical

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