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http://baderlab.org/Software/EnrichmentMap
Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together.
Proper citation: EnrichmentMap (RRID:SCR_016052) Copy
Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.
Proper citation: HyPhy (RRID:SCR_016162) Copy
https://github.com/sdparekh/zUMIs
Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information.
Proper citation: zUMIs (RRID:SCR_016139) Copy
Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences.
Proper citation: Fastml (RRID:SCR_016092) Copy
http://bioplex.hms.harvard.edu/
Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection.
Proper citation: BioPlex (RRID:SCR_016144) Copy
Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium.
Proper citation: mentha (RRID:SCR_016148) Copy
https://github.com/Oshlack/necklace/wiki
Software that combines reference and assembled transcriptomes for RNA-Seq analysis. It replaces many manual steps in the pipeline of RNA-Seq analyses involving species with incomplete genome or annotations.
Proper citation: Necklace (RRID:SCR_016103) Copy
http://zzlab.net/blink/index.html
Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power.
Proper citation: BLINK (RRID:SCR_016288) Copy
http://bioconductor.org/packages/release/bioc/html/MetaCyto.html
Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.
Proper citation: MetaCyto (RRID:SCR_016415) Copy
https://github.com/sblanck/smagexp
Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more.
Proper citation: SMAGEXP (RRID:SCR_016360) Copy
https://omictools.com/fluxmodecalculator-tool
Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: FluxModeCalculator (RRID:SCR_016290) Copy
Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines.
Proper citation: Lifebit Deploit (RRID:SCR_016428) Copy
Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets.
Proper citation: Microscopy Image Browser (RRID:SCR_016560) Copy
https://www.genome.jp/tools/dinies/
Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference.
Proper citation: DINIES (RRID:SCR_016505) Copy
https://github.com/WGS-TB/MentaLiST
Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.
Proper citation: MentaLiST (RRID:SCR_016469) Copy
Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
Proper citation: cisTEM (RRID:SCR_016502) Copy
https://pachterlab.github.io/kallisto/about
Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads.
Proper citation: kallisto (RRID:SCR_016582) Copy
http://www.ebi.ac.uk/~zerbino/oases/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
Proper citation: Oases (RRID:SCR_011896) Copy
http://tophat.cbcb.umd.edu/fusion_index.html
An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.
Proper citation: TopHat-Fusion (RRID:SCR_011899) Copy
http://cbcb.umd.edu/software/metAMOS
A modular and open source metagenomic assembly and analysis pipeline.
Proper citation: MetAMOS (RRID:SCR_011914) Copy
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