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http://lincsportal.ccs.miami.edu/dcic-portal/
Portal which provides a unified interface for searching LINCS dataset packages and reagents. Users can use the portal to access datasets, small molecules, cells, genes, proteins and peptides, and antibodies.
Proper citation: LINCS Data Portal (RRID:SCR_014939) Copy
https://github.com/kstreet13/slingshot
Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics.
Proper citation: Slingshot (RRID:SCR_017012) Copy
https://github.com/shendurelab/LACHESIS
Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies.
Proper citation: LACHESIS (RRID:SCR_017644) Copy
Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins.
Proper citation: PathVisio (RRID:SCR_023789) Copy
Software application for annotating character matrix files with ontology terms. Character states can be annotated using Entity-Quality syntax, where entity, quality, and possibly related entities are drawn from requisite ontologies. In addition, taxa (the rows of a character matrix) can be annotated with identifiers from taxonomy ontology. Phenex saves ontology annotations alongside original free text character matrix data using new NeXML format standard for evolutionary data.
Proper citation: Phenex (RRID:SCR_021748) Copy
https://www.bcgsc.ca/resources/software/ntcard
Software tool for estimating k-mer coverage histogram of genomics data. Streaming algorithm for estimating frequencies of k-mers in genomics datasets.
Proper citation: ntCard (RRID:SCR_022010) Copy
https://github.com/davidaknowles/leafcutter/
Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs).
Proper citation: LeafCutter (RRID:SCR_017639) Copy
https://github.com/sreeramkannan/Shannon
Software tool for de novo transcriptome assembly from RNA-Seq data.
Proper citation: Shannon (RRID:SCR_017037) Copy
https://github.com/hahnlab/CAFExp
Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny.
Proper citation: Computational Analysis of gene Family Evolution (RRID:SCR_018924) Copy
https://github.com/broadinstitute/Drop-seq
Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript.
Proper citation: Drop-seq tools (RRID:SCR_018142) Copy
https://bioconductor.org/packages/SNPRelate/
Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data.
Proper citation: SNPRelate (RRID:SCR_022719) Copy
https://github.com/xfengnefx/hifiasm-meta
Software tool as metagenome assembler that exploits high accuracy of recent data. De novo metagenome assembler, based on haplotype resolved de novo assembler for PacBio Hifi reads. Workflow consists of optional read selection, sequencing error correction, read overlapping, string graph construction and graph cleaning.
Proper citation: hifiasm-meta (RRID:SCR_022771) Copy
https://CRAN.R-project.org/package=ComplexUpset
Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries.
Proper citation: ComplexUpset (RRID:SCR_022752) Copy
https://github.com/FunctionLab/sei-framework
Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types.
Proper citation: sei (RRID:SCR_022571) Copy
Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets.
Proper citation: UpSet (RRID:SCR_022731) Copy
https://github.com/walaj/svaba
Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements.
Proper citation: SvABA (RRID:SCR_022998) Copy
https://upsetplot.readthedocs.io/en/stable/
Software Python implementation of UpSet plots to visualize set overlaps.
Proper citation: UpSetPlot (RRID:SCR_023225) Copy
Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track.
Proper citation: CRISPOR (RRID:SCR_015935) Copy
Web based tool to visualize gene expression and metadata annotation distribution throughout single cell dataset or multiple datasets. Interactive viewer for single cell expression. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster specific marker genes.
Proper citation: UCSC Cell Browser (RRID:SCR_023293) Copy
https://github.com/hetio/hetmatpy
Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes.
Proper citation: HetMatPy (RRID:SCR_023409) Copy
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