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Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines.
Proper citation: CMap (RRID:SCR_016204) Copy
https://github.com/HingeAssembler/HINGE
Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution.
Proper citation: Hinge (RRID:SCR_016135) Copy
https://github.com/soedinglab/hh-suite
Software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Used for sequence-based protein function and structure prediction what depends on sequence-search sensitivity and accuracy of the resulting sequence alignments.
Proper citation: HH-suite (RRID:SCR_016133) Copy
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
Proper citation: DESeq2 (RRID:SCR_015687) Copy
https://github.com/ruanjue/smartdenovo
Software tool as de novo assembler for PacBio and Oxford Nanopore data. It produces assembly from all-vs-all raw read alignments without error correction stage. Allows to read overlapping, rescue missing overlaps, identify low-quality regions and chimaera and produce better consensus.
Proper citation: SMARTdenovo (RRID:SCR_017622) Copy
https://www.rdocumentation.org/packages/pheatmap/versions/0.2/topics/pheatmap
Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters.
Proper citation: pheatmap (RRID:SCR_016418) Copy
Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).
Proper citation: FreeContact (RRID:SCR_016113) Copy
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
https://github.com/eead-csic-compbio/metagenome_Pfam_score
Open source software to evaluate, quantify, compare, and predict the metabolic machinery of interest in large ‘omic’ datasets. This protocol finds informative protein families and uses them to score metagenomic sets.
Proper citation: MEBS: Multigenomic Entropy-Based Score (RRID:SCR_015708) Copy
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
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
https://github.com/xavierdidelot/clonalorigin
Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.
Proper citation: ClonalOrigin (RRID:SCR_016061) Copy
https://bioconductor.org/packages/ReactomePA/
Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.
Proper citation: ReactomePA (RRID:SCR_019316) Copy
https://github.com/BNadel/GEDIT
Software tool for accurate cell type quantification from gene expression data. Uses gene expression data to estimate cell type abundances. Allows user to supply custom reference matrices.
Proper citation: GEDIT (RRID:SCR_019277) Copy
Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers.
Proper citation: ImJoy (RRID:SCR_020935) Copy
https://github.com/statOmics/tradeSeq
Software tool as suite of tests for identifying dynamic temporal gene regulation using single cell RNA-seq data.Trajectory based differential expression analysis for sequencing data.
Proper citation: tradeSeq (RRID:SCR_019238) Copy
http://srna-workbench.cmp.uea.ac.uk
Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals.
Proper citation: UEA sRNA Workbench (RRID:SCR_020947) Copy
http://bioinformatics.sdstate.edu/go/
Software graphical gene set enrichment tool for animals and plants. Graphical web application to gain insights from gene sets. Features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for retrieval of pathway diagrams and protein-protein interaction networks.
Proper citation: ShinyGO (RRID:SCR_019213) Copy
https://bioconductor.org/packages/biomaRt/
Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis.
Proper citation: biomaRt (RRID:SCR_019214) Copy
Software tool for phylogenomic inference.
Proper citation: IQ TREE (RRID:SCR_021163) Copy
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