Tools   Select Another Resource Report Type

https://github.com/TransDecoder/TransDecoder

Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.

Proper citation: TransDecoder (RRID:SCR_017647) Copy   

•   Source: SciCrunch Registry
  

https://www.sanger.ac.uk/science/tools/reapr

Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.

Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy   

•   Source: SciCrunch Registry
  

https://github.com/almorlio/CiLiQuant

Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance.

Proper citation: CiLiQuant (RRID:SCR_019319) Copy   

•   Source: SciCrunch Registry
  

https://qupath.github.io/

Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.

Proper citation: QuPath (RRID:SCR_018257) Copy   

•   Source: SciCrunch Registry
  

https://github.com/taborlab/FlowCal

Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.

Proper citation: FlowCal (RRID:SCR_018140) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ComparativeGenomicsToolkit/hal/tree/master/synteny

Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment.

Proper citation: halSynteny (RRID:SCR_018127) Copy   

•   Source: SciCrunch Registry
  

https://metacpan.org/dist/Bio-EUtilities

Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic.

Proper citation: Bio-EUtilities (RRID:SCR_024064) Copy   

•   Source: SciCrunch Registry
  

https://metacpan.org/dist/Bio-Tools-Run-Alignment-Clustalw

Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.

Proper citation: Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) Copy   

•   Source: SciCrunch Registry
  

https://metacpan.org/dist/Bio-Tools-Phylo-PAML

Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.

Proper citation: Bio-Tools-Phylo-PAML (RRID:SCR_024069) Copy   

•   Source: SciCrunch Registry
  

https://metacpan.org/dist/Bio-Graphics

Software package to generate GD images of Bio::Seq objects.

Proper citation: Bio-Graphics (RRID:SCR_024061) Copy   

•   Source: SciCrunch Registry
  

https://github.com/PacificBiosciences/pbcopper

Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications.

Proper citation: pbcopper (RRID:SCR_024152) Copy   

•   Source: SciCrunch Registry
  

https://github.com/genouest/biomaj-cli

Software package to use BioMAJ providing biomaj-cli.

Proper citation: CLI for BioMAJ (RRID:SCR_023980) Copy   

•   Source: SciCrunch Registry
  

https://github.com/GATB/bcalm

Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution.

Proper citation: BCALM 2 (RRID:SCR_023975) Copy   

•   Source: SciCrunch Registry
  

https://github.com/gpertea/gclib

Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time.

Proper citation: GCLib (RRID:SCR_024028) Copy   

•   Source: SciCrunch Registry
  

https://github.com/dutilh/CAT

Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies.

Proper citation: CAT and BAT (RRID:SCR_023988) Copy   

•   Source: SciCrunch Registry
  

https://github.com/RoelofBerg/limereg

Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image.

Proper citation: limereg (RRID:SCR_024097) Copy   

•   Source: SciCrunch Registry
  

https://github.com/xdf-modules/libxdf

Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications.

Proper citation: Libxdf (RRID:SCR_024096) Copy   

•   Source: SciCrunch Registry
  

https://github.com/mbillingr/libgdf

Software library for processing of biomedical signals. Provides generic storage for biosignals, such as EEG, ECG, MEG. C++ implementation of GDF - " general dataformat for biosignals" version V2.20.

Proper citation: libGDF (RRID:SCR_024075) Copy   

•   Source: SciCrunch Registry
  

https://github.com/husonlab/jloda

Software Java library of data structures and algorithms.Provides some basic data structures and algorithms used by SplitsTree, Dendroscope and MEGAN.

Proper citation: JLODA (RRID:SCR_024076) Copy   

•   Source: SciCrunch Registry
  

https://gitlab.com/german.tischler/libmaus2

Software collection of data structures and algorithms. Contains I/O classes (single byte and UTF-8), bitio classes (input, output and various forms of bit level manipulation), text indexing classes (suffix and LCP array, fulltext and minute (FM), ...), BAM sequence alignment files input/output (simple and collating) and many lower level support classes.

Proper citation: libmaus2 (RRID:SCR_024077) Copy   

•   Source: SciCrunch Registry