Tools   Select Another Resource Report Type

https://github.com/lkmklsmn/DrivAER

Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data.

Proper citation: DrivAER (RRID:SCR_019076) Copy   

•   Source: SciCrunch Registry

https://github.com/wilkinsonlab/epigenomics_pipeline

Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter.

Proper citation: Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/HighV-QUEST/home.action

Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing.

Proper citation: IMGT HighV-QUEST (RRID:SCR_018196) Copy   

•   Source: SciCrunch Registry

https://pm4ngs.readthedocs.io/

Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution.

Proper citation: PM4NGS (RRID:SCR_019164) Copy   

•   Source: SciCrunch Registry

https://github.com/ANGSD/ngsRelate

Software tool for estimating pairwise relatedness from next-generation sequencing data.

Proper citation: ngsRelate (RRID:SCR_016588) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html

Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.

Proper citation: ComplexHeatmap (RRID:SCR_017270) Copy   

•   Source: SciCrunch Registry

https://swissmodel.expasy.org/

Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists.

Proper citation: SWISS-MODEL (RRID:SCR_018123) Copy   

•   Source: SciCrunch Registry

https://signor.uniroma2.it/

Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles.

Proper citation: SIGNOR (RRID:SCR_018485) Copy   

•   Source: SciCrunch Registry

https://github.com/FRED-2/OptiType

Software tool for precision HLA typing from next generation sequencing data.

Proper citation: OptiType (RRID:SCR_022279) Copy   

•   Source: SciCrunch Registry

http://rrwick.github.io/Bandage/

Software tool for visualising de novo assembly graphs. By displaying connections which are not present in contigs file, opens up new possibilities for analysing de novo assemblies. Used for interactive visualization of de novo genome assemblies.

Proper citation: Bandage (RRID:SCR_022772) Copy   

•   Source: SciCrunch Registry

http://www.mricro.com

Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.

Proper citation: MRIcron (RRID:SCR_002403) Copy   

•   Source: SciCrunch Registry

https://github.com/Brazelton-Lab/seq-annot

Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes.

Proper citation: seq-annot (RRID:SCR_018731) 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://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://sourceforge.net/projects/tab2mage/

Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.

Proper citation: Tab2MAGE (RRID:SCR_024101) 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

http://colibread.inria.fr/software/mapsembler2/

Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.

Proper citation: Mapsembler2 (RRID:SCR_024102) Copy   

•   Source: SciCrunch Registry

https://github.com/gerddie/maxflow

Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph.

Proper citation: MAXFLOW (RRID:SCR_024103) 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