Tools   Select Another Resource Report Type

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/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://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

http://tools.neb.com/NEBcutter2/

This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and submit. Further options will appear with the output. The maximum size of the input file is 1 MByte, and the maximum sequence length is 300 KBases. NEBcutter produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://rebase.neb.com/rebase/rebase.html). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini.

Proper citation: NEBcutter (RRID:SCR_010664) Copy   

•   Source: SciCrunch Registry

http://www.benoslab.pitt.edu/comir/

Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.

Proper citation: ComiR (RRID:SCR_013023) Copy   

•   Source: SciCrunch Registry

http://tools.genxpro.net/omiras/

A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions.

Proper citation: omiRas (RRID:SCR_010833) Copy   

•   Source: SciCrunch Registry

http://www.mutationtaster.org/

Evaluates disease-causing potential of sequence alterations.

Proper citation: MutationTaster (RRID:SCR_010777) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/EGSEA/

Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets.

Proper citation: EGSEA (RRID:SCR_015036) Copy   

•   Source: SciCrunch Registry

http://gump.qimr.edu.au/general/daleN/SNPSpD/

SNPSpD is a method of correcting for non-independance of single nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of LD between SNP''s. Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.

Proper citation: Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) (RRID:SCR_008621) Copy   

•   Source: SciCrunch Registry

http://www.genoread.org/

A sequence verification pipeline where users can submit trace files to verify if a clone''s physical sequence matches its reference sequence.

Proper citation: GenoREAD (RRID:SCR_012007) Copy   

•   Source: SciCrunch Registry

http://dsap.cgu.edu.tw/

A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DSAP (RRID:SCR_013352) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/fdr/

Software application (entry from Genetic Analysis Software)

Proper citation: WEIGHTED FDR (RRID:SCR_013442) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/ssaha2-0

A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported.

Proper citation: Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) Copy   

•   Source: SciCrunch Registry

http://alchemy.sourceforge.net/

ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed.

Proper citation: ALCHEMY (RRID:SCR_005761) Copy   

•   Source: SciCrunch Registry

http://bamview.sourceforge.net/

A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub.

Proper citation: BamView (RRID:SCR_004207) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/genomedata/

A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.

Proper citation: Genomedata (RRID:SCR_004544) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.uni-leipzig.de/Software/RNAplex/

Software tool to rapidly search for short interactions between two long RNAs.

Proper citation: RNAplex (RRID:SCR_002763) Copy   

•   Source: SciCrunch Registry