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Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences.
Proper citation: Atac (RRID:SCR_015980) Copy
https://github.com/pezmaster31/bamtools/wiki
Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.
Proper citation: Bamtools (RRID:SCR_015987) Copy
https://bioconductor.org/packages/release/bioc/html/scater.html
Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.
Proper citation: scater (RRID:SCR_015954) Copy
http://sing.ei.uvigo.es/ALTER/
Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.
Proper citation: ALTER (RRID:SCR_015968) Copy
http://www.atgc-montpellier.fr/lordec/
Software that performs hybrid error correction for long, PacBio reads. LoRDEC can correct insertions, deletions, and substitutions in PacBio reads.
Proper citation: LoRDEC (RRID:SCR_015814) Copy
http://ualcan.path.uab.edu/cgi-bin/ualcan-res.pl
Web application and database for analyzing cancer transcriptome data. It also has applications is facilitating tumor subgroup gene expression and survival analyses.
Proper citation: UALCAN (RRID:SCR_015827) Copy
http://app.cgu.edu.tw/circlnc/
Web application for mapping functional networks of long or circular forms of non-coding RNAs. It supports the uploading and processing of user-defined NGS-based gene expression matrix data.
Proper citation: circlncRNAnet (RRID:SCR_015794) Copy
http://gigadb.org/dataset/100360
Method for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets.
Proper citation: VaDiR (RRID:SCR_015797) Copy
https://www.github.com/arq5x/poretools
Software toolkit for analyzing nanopore sequence data.
Proper citation: Poretools (RRID:SCR_015879) Copy
https://swisstree.vital-it.ch/
Project that aims to provide a collection of Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure.
Proper citation: SwissTree (RRID:SCR_015881) Copy
Web application that is a phylogenetic tree viewer based on d3.js. It was developed as an alternative to Archaeopteryx inspired by d3.phylogram.js.
Proper citation: PhyD3 (RRID:SCR_015892) Copy
Perl software for transcription factor binding site detection and analysis. It implements classes for the representation of objects encountered in analysis of these protein-binding sites.
Proper citation: TFBS (RRID:SCR_015774) Copy
https://github.com/jts/nanopolish
Software package for signal-level analysis of Oxford Nanopore sequencing data.
Proper citation: Nanopolish (RRID:SCR_016157) Copy
https://github.com/bbuchfink/diamond
Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.
Proper citation: DIAMOND (RRID:SCR_016071) Copy
IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application.
Proper citation: IDEPI - IDentify EPItopes (RRID:SCR_016171) Copy
https://github.com/genomeannotation/GAG
Command line program to read, modify, annotate and generate genomic data. Can write files to .gff3 or to the NCBI's .tbl format.
Proper citation: Genome Annotation Generator (RRID:SCR_016053) Copy
https://github.com/sorgerlab/ashlar
Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration.
Proper citation: ASHLAR (RRID:SCR_016266) Copy
Software for syntax highlighting for computational biology.
Proper citation: bioSyntax (RRID:SCR_016207) Copy
Software as an open source machine learning framework for everyone. Library for high performance numerical computation. Allows deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices.
Proper citation: tensorflow (RRID:SCR_016345) Copy
https://odmltables.readthedocs.io
Software that facilitates the handling of metadata collections stored in the odML format. Some supported operations include reduction, merging of odml structures, and the conversion from the hierarchical odML format to tabular formats.
Proper citation: odMLtables (RRID:SCR_016228) Copy
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