Tools   Select Another Resource Report Type

https://github.com/mahmoudibrahim/JAMM

Software tool as peak finder for joint analysis of NGS replicates. Used for peak finding in next generation sequencing broad and narrow datasets like ChIP-Seq, ATAC-Seq, DNase-Seq. Can integrate information from biological replicates and assign peak boundaries accurately.

Proper citation: JAMM (RRID:SCR_017049) Copy   

•   Source: SciCrunch Registry

http://srv00.recas.ba.infn.it/atlas/index.html

Comprehensive database of A-to-I RNA Editing Events. Atlas of A-to-I RNA editing events in human and other organisms. Collection of A-to-I events in body sites of healthy individuals from GTEx project. RNA Editing sites can be searched by genomic region, gene name and other relevant features as tissue of origin. Query results are shown in sortable and downloadable tables in which main characteristics of individual RNA editing events are reported. RNA-Seq and DNA-Seq coverage per site as well as RNA editing levels are provided.

Proper citation: REDIportal (RRID:SCR_018490) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/NetPhos/

Web tool as artificial neural network method that predicts phosphorylation sites in independent sequences. Web application based on determination of activity of protein kinases using in vitro assays with either naturally occurring peptides or synthetic peptides. NetPhos 3.1 server predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. Generic predictions are identical to predictions performed by NetPhos 2.0. Kinase specific predictions are identical to predictions by NetPhosK 1.0. NetPhos 3.1 is available as stand-alone software package.

Proper citation: NetPhos (RRID:SCR_017975) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.uni-muenster.de/tools/nanopipe2

Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms.

Proper citation: NanoPipe (RRID:SCR_016852) Copy   

•   Source: SciCrunch Registry

http://deweylab.biostat.wisc.edu/detonate/

Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences.

Proper citation: DETONATE (RRID:SCR_017035) Copy   

•   Source: SciCrunch Registry

http://www.cazy.org

Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site.

Proper citation: CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/ProP/

Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction.

Proper citation: ProP Server (RRID:SCR_014936) Copy   

•   Source: SciCrunch Registry

http://www.cprofiler.org/

Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output.

Proper citation: Composition Profiler (RRID:SCR_014630) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/psa/genewise/

Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool.

Proper citation: GeneWise (RRID:SCR_015054) Copy   

•   Source: SciCrunch Registry

http://openbabel.org/wiki/Main_Page

Software toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats.

Proper citation: Open Babel (RRID:SCR_014920) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://www.gencodegenes.org

Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.

Proper citation: GENCODE (RRID:SCR_014966) Copy   

•   Source: SciCrunch Registry

https://xia2.github.io/

Data processing software that performs X-ray diffraction data processing. It handles multi-pass, multi-wavelength data sets and supports remote access to synchrotron facilities.

Proper citation: xia2 pipeline (RRID:SCR_015746) Copy   

•   Source: SciCrunch Registry

http://cab.spbu.ru/software/rnaquast/

Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software.

Proper citation: rnaQUAST (RRID:SCR_016994) Copy   

•   Source: SciCrunch Registry

http://oufti.org/

Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions.

Proper citation: Oufti (RRID:SCR_016244) Copy   

•   Source: SciCrunch Registry

https://urgi.versailles.inra.fr/Tools/PASTEClassifier

Software tool for automatic transposable element classification. Used for searching for structural features and similarity to classify transposable elements.

Proper citation: PASTEClassifier (RRID:SCR_017645) Copy   

•   Source: SciCrunch Registry

https://github.com/fritzsedlazeck/Sniffles

Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates.

Proper citation: Sniffles (RRID:SCR_017619) Copy   

•   Source: SciCrunch Registry

https://github.com/voutcn/megahit

Software tool as Next Generation Sequencing assembler. Optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single cell assembly. Can assemble genome sequences from metagenomic datasets of hundreds of Giga base-pairs in time and memory efficient manner on single server.

Proper citation: MEGAHIT (RRID:SCR_018551) Copy   

•   Source: SciCrunch Registry

https://github.com/BGI-Qingdao/TGS-GapCloser

Software tool that uses long reads to enhance genome assembly. Fast and accurate gap closing software tool that uses low coverage of error-prone long reads generated by third generation sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs for large genomes.

Proper citation: TGS-GapCloser (RRID:SCR_017633) Copy   

•   Source: SciCrunch Registry

https://github.com/AnacletoLAB/parSMURF

Open source software package as high performance computing imbalance aware machine learning tool for genome wide detection of pathogenic variants.

Proper citation: parSMURF (RRID:SCR_017560) Copy   

•   Source: SciCrunch Registry

https://github.com/hms-dbmi/EHRtemporalVariability

Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users.

Proper citation: EHRtemporalVariability (RRID:SCR_018663) Copy   

•   Source: SciCrunch Registry