Tools   Select Another Resource Report Type

http://multiqc.info/

Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python.

Proper citation: MultiQC (RRID:SCR_014982) Copy   

•   Source: SciCrunch Registry
  

https://www.gnu.org/software/octave/

A high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments. It may also be used as a batch-oriented language. Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, functions written in the Octave language, or by using dynamically loaded modules written in C, C++, Fortran, or other languages., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GNU Octave (RRID:SCR_014398) Copy   

•   Source: SciCrunch Registry
  

https://cibersort.stanford.edu/

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

Proper citation: CIBERSORT (RRID:SCR_016955) Copy   

•   Source: SciCrunch Registry
  

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry
  

http://www.atgc-montpellier.fr/phyml/

Web phylogeny server based on the maximum-likelihood principle.

Proper citation: PhyML (RRID:SCR_014629) Copy   

•   Source: SciCrunch Registry
  

http://abacas.sourceforge.net

Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account.

Proper citation: ABACAS (RRID:SCR_015852) Copy   

•   Source: SciCrunch Registry
  

http://rloop.bii.a-star.edu.sg/?pg=qmrlfs-finder

A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis.

Proper citation: QmRLFS-finder (RRID:SCR_014584) Copy   

•   Source: SciCrunch Registry
  

http://www.funrich.org/

A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts.

Proper citation: FunRich: Functional Enrichment analysis tool (RRID:SCR_014467) Copy   

•   Source: SciCrunch Registry
  

http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX

Software for protein domain search. It is a part of Embassy software package.

Proper citation: DOMAINATRIX (RRID:SCR_016084) Copy   

•   Source: SciCrunch Registry
  

https://git.metabarcoding.org/obitools/ecopcr/wikis/home

Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Ecopcr (RRID:SCR_016082) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/release/bioc/html/topGO.html

Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Proper citation: topGO (RRID:SCR_014798) Copy   

•   Source: SciCrunch Registry
  

https://github.com/rbutleriii/Clinotator

Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics.

Proper citation: Clinotator (RRID:SCR_016054) Copy   

•   Source: SciCrunch Registry
  

https://sites.google.com/site/danposdoc/

Software toolkit with various functions for the analysis of nucleosome and protein occupancy by sequencing.

Proper citation: DANPOS2 (RRID:SCR_015527) Copy   

•   Source: SciCrunch Registry
  

http://compbio.cs.princeton.edu/concavity/

Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets.

Proper citation: Concavity (RRID:SCR_016063) Copy   

•   Source: SciCrunch Registry
  

https://github.com/HASTE-project

Software toolkit for rapid development of cloud native intelligent data pipelines for scientific data streams. Hierarchical approach to acquisition, analysis, and interpretation of image data. Developed in the project Hierarchical Analysis of Spatial and Temporal Data.

Proper citation: HASTE-project (RRID:SCR_020932) Copy   

•   Source: SciCrunch Registry
  

https://mermaid.readthedocs.io/en/latest/

Registration toolbox written in pyTorch. Supports various image registration methods. Focuses on nonparametric registration approaches including stationary velocity fields and large discplacement diffeomorphic metric mapping models though simple affine registration is also possible. Allows for rapid prototyping of new image registration approaches and similarity measures.

Proper citation: MERMAID (RRID:SCR_020939) Copy   

•   Source: SciCrunch Registry
  

https://github.com/theislab/scvelo

Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling.

Proper citation: scVelo (RRID:SCR_018168) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Ecogenomics/GtdbTk

Open source software tool for assigning objective taxonomic classifications to bacterial and archaeal genomes based on Genome Database Taxonomy. Designed to work with recent advances that allow metagenome assembled genomes to be obtained directly from environmental samples. Can also be applied to isolate and single cell genomes.

Proper citation: GTDB-Tk (RRID:SCR_019136) Copy   

•   Source: SciCrunch Registry
  

https://github.com/marbl/Mash

Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.

Proper citation: Mash (RRID:SCR_019135) Copy   

•   Source: SciCrunch Registry
  

http://www.pyrosetta.org/

Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions.

Proper citation: PyRosetta (RRID:SCR_018541) Copy   

•   Source: SciCrunch Registry