Search results

• Pomoxis
  Pomoxis started life as a set of services to perform analysis of squiggles as draft assemblies. Many of these tools are used by the research data analysis
  2 KB (285 words) - 18:48, 21 August 2022
• Biolite
  ...cks provenance, and provides lightweight tools for building out customized analysis pipelines. * A 'catalog' database for pairing metadata with and organizing NGS data files.
  3 KB (362 words) - 12:54, 15 August 2022
• RepeatExplorer
  uses high-throughput genome sequencing data as an input and performs graph-based clustering analysis of sequence read similarities to identify
  2 KB (278 words) - 21:44, 21 August 2022
• VDJtools
  ...mprehensive analysis framework for T-cell and B-cell repertoire sequencing data. ...le?id=10.1371/journal.pcbi.1004503 Shugay M et al. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comp Biol 2015; 11(11):e1004503-e10045
  2 KB (280 words) - 21:29, 6 December 2019
• TREEPUZZLE
  ...es. The corresponding parameters (except for GTR) can be inferred from the data set. ...n, and A. von Haeseler (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 18:502-504.]
  4 KB (450 words) - 19:31, 10 June 2022
• CellRanger-ARC
  ...erential analysis, and feature linkage between peaks and genes that aid in data interpretation.
  3 KB (288 words) - 18:24, 12 August 2022
• CGATools
  ...urce project to provide tools for downstream analysis of Complete Genomics data. The focus is to provide command line utilities, but a C++ API is available
  2 KB (291 words) - 13:26, 15 August 2022
• Circos
  ...is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationship ...fographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure t
  3 KB (409 words) - 13:35, 15 August 2022
• Bactopia
  ...ete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses Petit III RA, Read TD, Bactopia: a flexible pipeline for complete analysis of bacterial genomes. mSystems. 5 (2020), https://doi.org/10.1128/mSystems.
  2 KB (292 words) - 21:38, 10 January 2023
• Rvtests
  ...Rare Variant tests, is a flexible software package for genetic association analysis for sequence datasets. ...nd Comprehensive Tool for Rare Variant Association Analysis Using Sequence Data. Bioinformatics 2016 32: 1423-1426.]
  3 KB (293 words) - 21:59, 21 August 2022
• Biopieces
  ...downstream Biopieces until the data stream is terminated at the end of the analysis as outlined below: * BP_DATA - biopieces data directory
  3 KB (410 words) - 15:40, 10 December 2021
• BEAGLE
  ...is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of sample *phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs,
  5 KB (615 words) - 15:36, 14 December 2022
• QTLtools
  ...olecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-pe ...068635 Delaneau et al. A complete tool set for molecular QTL discovery and analysis.]
  2 KB (297 words) - 20:58, 21 August 2022
• Healthcare and Life Sciences
  ...science, including medical image analysis, disease detection, and genomic data interpretation, through [https://support.rc.ufl.edu/ support requests] or [ ...very that simplifies and accelerates the training of models using your own data and scaling the deployment of models for drug discovery applications.
  4 KB (521 words) - 16:00, 14 May 2024
• Biology
  ..., in our turn, will provide the hardware and software support for the data analysis pipeline they create for you. ...T databases, which serve both Galaxy and the command line blast see <code>/data/reference/blast/db</code>.
  4 KB (665 words) - 21:23, 14 December 2022
• HTSeq
  HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. ...ntation chapter A tour through HTSeq] first for an overview on the kind of analysis you can do with HTSeq and the design of the package, and then look at the r
  3 KB (411 words) - 19:05, 12 August 2022
• Lima
  ...ltiplexing. This new tool provides a better end-to-end user experience for analysis of multiplexed samples.
  3 KB (299 words) - 19:57, 15 August 2022
• Gephi
  ...ecognized to facilitate reasoning. This is a software for Exploratory Data Analysis, a paradigm appeared in the Visual Analytics field of research.
  3 KB (337 words) - 17:42, 11 January 2023
• CellRanger
  ...ds, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 supports libraries generated by the Chromium Single Cell 3 * HPC_{{uc:{{#var:app}}}}_REF - reference data directory
  2 KB (294 words) - 18:24, 12 August 2022
• RepeatAnalysisTools
  This repository contains instructions for processing and repeat analysis of sequence data generated with the PacBio No-Amp Targeted Sequencing
  4 KB (430 words) - 16:55, 15 December 2022
• PGDSpider
  ...meters or statistics for specific regions, and thus perform sliding window analysis over large genomic regions. ...t/28/2/298.full Lischer HEL and Excoffier L (2012) PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs. B
  3 KB (387 words) - 19:04, 10 June 2022
• QualiMap
  ...d-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. *rnaseq - Evaluate RNA-seq alignment data
  3 KB (326 words) - 19:32, 24 August 2022
• Pyrpipe
  ...ed on local computers or on HPC environments to manage analysis of RNA-Seq data. Users can use the easy-to-use APIs to popular bioinformatic tools provided
  3 KB (311 words) - 15:22, 16 March 2020
• GWAMA
  ...tions via meta-analysis, without direct exchange of genotype and phenotype data. ...11-288 Magi R, Morris AP: GWAMA: software for genome-wide association meta-analysis. BMC Bioinformatics 2010, 11:288.]
  3 KB (322 words) - 13:33, 26 May 2020
• ClinicaDL
  ...th neurological and psychiatric diseases and the acquisition of multimodal data (neuroimaging, clinical and cognitive evaluations, genetics...), most often ...x, PETPVC, SPM), machine learning (Scikit-learn) and the BIDS standard for data organization.
  3 KB (323 words) - 13:41, 15 August 2022
• GenGen
  ...free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated. .../S0002-9297(07)63775-6 Wang K, Li M, Bucan M. Pathway-based approaches for analysis of genome-wide association studies. American Journal of Human Genetics, 81:
  3 KB (326 words) - 17:36, 10 June 2022
• Alphaimpute
  ...bForAlphaImpute (Kerr and Kinghorn, 1996). All information on the model of analysis, input files and their layout, is specified in a single parameter file.
  3 KB (337 words) - 12:37, 12 August 2022
• Ssr pipeline
  ...llites conforming to user specified parameters. Each of the three separate analysis modules also can be used independently to provide greater flexibility or to ...ughput DNA sequence data (ver. 1.1, February 2014): U.S. Geological Survey Data Series 778.
  4 KB (501 words) - 18:55, 6 June 2022
• REMORA
  [[Category:Software]][[Category:Performance Analysis]][[Category:Performance Analysis]] * CPU Power and Temperature data
  3 KB (330 words) - 20:39, 24 August 2022
• LIQA
  LIQA (Long-read Isoform Quantification and Analysis) is an Expectation-Maximization alternative splicing (DAS) events using long-read RNA-seq data. LIQA incorporates
  3 KB (319 words) - 20:03, 15 August 2022
• Knime
  [[Category:Data Science]] ...-code interface offers an easy introduction for beginners, and an advanced data science set of tools for experienced users.
  3 KB (318 words) - 14:46, 9 June 2023
• QIIME
  ...from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has b
  4 KB (555 words) - 15:15, 19 August 2022
• Metabin
  ...nstructing a taxonomic tree of the results, and for performing comparative analysis of the taxonomic profiles for multiple metagenomic datasets.
  4 KB (588 words) - 19:25, 18 August 2022
• Pypaftol
  ...applicable and hopefully useful beyond PAFTOL, e.g. for processing HybSeq data in general. Functionality can be accessed either via the paftools script or
  3 KB (307 words) - 14:11, 9 April 2024
• LDhat
  ...languages for the analysis of recombination rates from population genetic data. The package is available either as C/C++ source code. *convert: Simple manipulation of DNA sequence data
  2 KB (296 words) - 17:09, 10 June 2022
• MEGA
  Molecular Evolutionary Genetics Analysis Software suite for analyzing DNA and protein sequence data from species and populations.
  3 KB (337 words) - 20:30, 15 December 2020
• Trans-ABySS
  De novo assembly of RNAseq data using ABySS ....html Robertson, G., et al. 2010. De novo assembly and analysis of RNA-seq data. Nature Methods 7, 909-912(2010)]
  2 KB (260 words) - 15:39, 10 June 2022
• Biodiverse
  Biodiverse is a tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic, trait and matr ...W., Lubarsky, E. & Rosauer, D.F. (2010) Biodiverse, a tool for the spatial analysis of biological and related diversity. Ecography. Vol 33, 643-647 (Version 1.
  3 KB (329 words) - 21:03, 6 December 2019
• Cgmaptools
  ...es in SNV, ASM and DMR. Command-line Toolset for Bisulfite Sequencing Data Analysis
  2 KB (264 words) - 21:01, 6 December 2019
• Parabricks
  .... The core of the Parabricks software is its data pipeline which takes raw data and transforms it according to the user's requirements. # Set data directories
  4 KB (574 words) - 21:25, 14 December 2022
• GDC-Client
  |{{#vardefine:url|https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool}} ...Atlas (TCGA) reach sizes of 200-300 GB. In such cases, a high performance data download and submission client is essential.
  3 KB (311 words) - 18:57, 12 August 2022
• PanX
  |{{#vardefine:url|https://github.com/neherlab/pan-genome-analysis}} ...notated bacterial strains as input (e.g. NCBI RefSeq records or user's own data in GenBank format). Alls genes from all strains are compared to each other
  3 KB (346 words) - 21:22, 6 December 2019
• Saffrontree
  ...tering of the data. It support NGS data (such as Illumina), 3rd generation data (Pacbio/Nanopore) and assembled sequences (FASTA).
  3 KB (400 words) - 17:17, 31 May 2022
• Scikit-learn
  ...nd data mining. It provides simple and efficient tools for predictive data analysis. scikit-learn is built on NumPy, SciPy, and matplotlib, and is open source
  2 KB (272 words) - 21:23, 6 March 2024
• BUCKy
  ...much of the genome supports each relationship, using Bayesian concordance analysis. BUCKy does not assume that genes (or loci) all have the same topology. Ins ...CKy: Gene tree / species tree reconciliation with the Bayesian concordance analysis. Bioinformatics (advance access).]
  3 KB (386 words) - 13:15, 15 August 2022
• Amphora2
  * HPC_{{uc:{{#var:app}}}}_EXE - test data directory * HPC_{{uc:{{#var:app}}}}_TAX- taxonomy data directory
  3 KB (333 words) - 17:35, 10 June 2022
• XWAS
  ...ally dimorphic characteristics. Special attention needs to be given to the analysis of X due to its unique inheritance pattern and X-inactivation. These analyt ...ddanda A, Ma L, Guo Y, Zhou Z, Keinan A. "XWAS: a toolset for genetic data analysis and association studies of the X chromosome." Journal of Heredity. 2015;106
  3 KB (383 words) - 13:27, 31 August 2020
• HPG Data Management
  ...earch analyses you need to [[Transfer_Data|upload]] and [[Storage|manage]] data. Note that misuse of the storage systems is the second main reason for acco ===Transferring Data===
  4 KB (587 words) - 19:27, 15 April 2023
• Fanc
  FAN-C provides a pipeline for analysing Hi-C data starting at mapped paired-end sequencing reads. ...work for the analysis and visualisation of chromosome conformation capture data. ''Genome Biol'' 21, 303. https://doi.org/10.1186/s13059-020-02215-9
  2 KB (281 words) - 15:56, 22 March 2024
• Strelka
  ...el improves on the original Strelka method for liquid and late-stage tumor analysis by accounting for possible tumor cell contamination in the normal sample. A
  3 KB (369 words) - 14:24, 10 October 2023

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