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https://pachterlab.github.io/sleuth/about
Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance.
Proper citation: sleuth (RRID:SCR_016883) Copy
http://www.bioconductor.org/packages/release/bioc/html/ropls.html
Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables.
Proper citation: ropls (RRID:SCR_016888) Copy
https://github.com/flo-compbio/xlmhg
Software Python package as a semiparametric test for enrichment in ranked lists. Used for determining gene set enrichment.
Proper citation: XL-mHG (RRID:SCR_016846) Copy
Software framework for image processing to obtain 3D models of macromolecular complexes using Electron Microscopy. Open-source project for integration, reproducibility and validation in 3D electron microscopy. It integrates several software packages to execute workflows combining different software tools, while taking care of formats and conversions. Electron Microscopy (3DEM). waiting for pdf from Joe
Proper citation: SCIPION (RRID:SCR_016738) Copy
https://github.com/TGAC/RAMPART
Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems.
Proper citation: Rampart (RRID:SCR_016742) Copy
https://panoramaweb.org/project/home/begin.view?
Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents.
Proper citation: PanoramaWeb (RRID:SCR_017136) Copy
Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs.
Proper citation: BSA4Yeast (RRID:SCR_017113) Copy
https://knights-lab.github.io/MLRepo/
Machine learning repository for microbiome datasets.
Proper citation: ML Repo (RRID:SCR_017079) Copy
https://github.com/tseemann/shovill
Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit.
Proper citation: shovill (RRID:SCR_017077) Copy
https://github.com/PGB-LIV/VAPPER
Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections.
Proper citation: VAPPER (RRID:SCR_016993) Copy
https://github.com/CGATOxford/UMI-tools
Open source software package for handling Unique Molecular Identifiers in NGS data sets.
Proper citation: UMI-tools (RRID:SCR_017048) Copy
http://cab.spbu.ru/software/rnaspades/
Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9.
Proper citation: rnaSPAdes (RRID:SCR_016992) Copy
https://bioconductor.org/packages/release/bioc/html/goseq.html
Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies.
Proper citation: Goseq (RRID:SCR_017052) Copy
http://bioconductor.org/packages/GenomicRanges/
Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.
Proper citation: Genomic Ranges (RRID:SCR_017051) Copy
https://combine-lab.github.io/salmon/
Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias.
Proper citation: Salmon (RRID:SCR_017036) Copy
https://github.com/fmaguire/Bridger_Assembler
Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.
Proper citation: Bridger (RRID:SCR_017039) Copy
https://github.com/dgrun/FateID
Software R package for inference of cell fate bias from single cell RNA-seq data. Iterative supervised learning algorithm for probabilistic quantification of cell fate bias in progenitor populations.
Proper citation: FateID (RRID:SCR_017244) Copy
https://github.com/powellgenomicslab/ascend
Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions.
Proper citation: ascend (RRID:SCR_017257) Copy
Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference.
Proper citation: IQ-TREE (RRID:SCR_017254) Copy
https://www.ebi.ac.uk/Tools/psa/emboss_matcher/
Software tool for pairwise sequence alignment. Identifies local similarities in two input sequences. One of EMBL-EBI search and sequence analysis tools.
Proper citation: EMBOSSMatcher (RRID:SCR_017252) Copy
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