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https://sites.google.com/site/jingyijli/SLIDE.zip

Software package that takes exon boundaries and RNA-Seq data as input to discern the set of mRNA isoforms that are most likely to present in an RNA-Seq sample. It is based on a linear model with a design matrix that models the sampling probability of RNA-Seq reads from different mRNA isoforms. To tackle the model unidentifiability issue, SLIDE uses a modified Lasso procedure for parameter estimation. Compared with deterministic isoform assembly algorithms (e.g., Cufflinks), SLIDE considers the stochastic aspects of RNA-Seq reads in exons from different isoforms and thus has increased power in detecting more novel isoforms. Another advantage of SLIDE is its flexibility of incorporating other transcriptomic data such as RACE, CAGE, and EST into its model to further increase isoform discovery accuracy. SLIDE can also work downstream of other RNA-Seq assembly algorithms to integrate newly discovered genes and exons. Besides isoform discovery, SLIDE sequentially uses the same linear model to estimate the abundance of discovered isoforms.

Proper citation: SLIDE (RRID:SCR_005137) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/genome_bio/siphy/

Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions.

Proper citation: SiPhy (RRID:SCR_000564) Copy   

•   Source: SciCrunch Registry

http://phenex.phenoscape.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/mouseportal/

Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.

Proper citation: Sanger Mouse Resources Portal (RRID:SCR_006239) Copy   

•   Source: SciCrunch Registry

https://github.com/genome/bam-readcount

Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads.

Proper citation: bam readcount (RRID:SCR_023653) Copy   

•   Source: SciCrunch Registry

https://github.com/churchmanlab/genewalk

Software for individual genes functions determination that are relevant in particular biological context and experimental condition. Quantifies similarity between vector representations of gene and annotated GO terms through representation learning with random walks on condition specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks.

Proper citation: GeneWalk (RRID:SCR_023787) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/somalier

Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches.

Proper citation: somalier (RRID:SCR_028167) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://picrust.github.io/picrust/

Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome.

Proper citation: PICRUSt (RRID:SCR_016855) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/dkessner/forqs

Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits.

Proper citation: forqs (RRID:SCR_000643) Copy   

•   Source: SciCrunch Registry

https://github.com/bcgsc/NanoSim

Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software.

Proper citation: NanoSim (RRID:SCR_018243) Copy   

•   Source: SciCrunch Registry

http://khmer.readthedocs.org/

Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform.

Proper citation: khmer (RRID:SCR_001156) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

Proper citation: Bioconductor (RRID:SCR_006442) Copy   

•   Source: SciCrunch Registry

https://github.com/smithlabcode/riborex

Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency.

Proper citation: riborex (RRID:SCR_019104) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Maaslin2.html

SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features.

Proper citation: MaAsLin2 (RRID:SCR_023241) Copy   

•   Source: SciCrunch Registry

https://www.cbcb.umd.edu/software/epiviz

Software package as interactive visualization tool for functional genomics data. Interactive visual analytics for functional genomics data.

Proper citation: Epiviz (RRID:SCR_022796) Copy   

•   Source: SciCrunch Registry

https://github.com/ParkerLab/ataqv

Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments.

Proper citation: ataqv (RRID:SCR_023112) Copy   

•   Source: SciCrunch Registry

https://github.com/fritzsedlazeck/SURVIVOR

Software tool set for simulating and evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs. Used for for SV simulation, comparison and filtering.

Proper citation: SURVIVOR (RRID:SCR_022995) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/merqury

Software toolkit for reference free quality, completeness, and phasing assessment for genome assemblies. Genome assembly quality evaluation based on k-mers.

Proper citation: Merqury (RRID:SCR_022964) Copy   

•   Source: SciCrunch Registry