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Web server for protein structure prediction and refinement. Used to predict protein structure from sequence by template based modeling. Used for refinement after providing starting model structure and locations of loops or termini to be refined.
Proper citation: GalaxyWEB (RRID:SCR_018558) Copy
http://emboss.bioinformatics.nl/cgi-bin/emboss/pepwheel
Web tool to visualise protein sequences as helices. Draws helical wheel diagram for protein sequence. EMBOSS pepwheel displays peptide sequences in helical representation.
Proper citation: pepwheel (RRID:SCR_018398) Copy
http://www.cbs.dtu.dk/services/MaxAlign/
Web tool for maximizing usable data in alignment. Maximizes number of characters that are present in gap free columns alignment area by selecting optimal subset of sequences. Removes sequences with many gaps in post process of alignments in order to improve alignment area.
Proper citation: MaxAlign (RRID:SCR_018552) Copy
http://huanglab.phys.hust.edu.cn/hpepdock/
Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations.
Proper citation: HPEPDOCK Server (RRID:SCR_018561) Copy
Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models.
Proper citation: BcForms (RRID:SCR_018654) Copy
http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE
Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation.
Proper citation: GalaxyRefine (RRID:SCR_018531) Copy
https://cran.r-project.org/web/packages/EpiEstim/index.html
Framework and software to estimate time varying reproduction numbers during epidemics. Tools to quantify transmissibility throughout epidemic from analysis of time series of incidence. Used to estimate time varying instantaneous reproduction numbers from incidence time series.
Proper citation: EpiEstim (RRID:SCR_018538) Copy
https://cran.r-project.org/package=precrec
Software R package for fast and accurate precision recall and ROC curve calculations. Calculates accurate precision recall and Receiver Operator Characteristics curves.
Proper citation: precrec (RRID:SCR_018659) Copy
Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition.
Proper citation: Datanator (RRID:SCR_018651) Copy
https://cm.jefferson.edu/Off-Spotter//
Web application that identifies genomic instances for a given combination of gRNA(s), PAM, number of mismatches, and seed. This tool is limited to a single 1,000 nucleotides sequence or fewer than twenty CR-separated 20-mers.
Proper citation: Off-Spotter (RRID:SCR_015739) Copy
http://amp.pharm.mssm.edu/gen3va/
Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme.
Proper citation: GEN3VA (RRID:SCR_015682) Copy
Software toolkit that provides several multi-modal tools to assess brain disconnections and remote effects of lesions. All modules are designed to process brain lesion data with a normalization algorithm, a module to estimate the probability and the severity of white matter disconnections, and a tool to build a map of the disconnected areas.
Proper citation: BCBtoolkit (RRID:SCR_015519) Copy
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://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
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