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• 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
• CASAVA
  Creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. ...can create genomic builds, call SNPs, detects indels, and count reads from data generated from one or more runs of the Genome Analyzer across a broad range
  3 KB (340 words) - 18:23, 12 August 2022
• AMPtk
  ...be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons.
  2 KB (289 words) - 12:41, 12 August 2022
• Slamdunk
  ...oftware tool for automated, robust, scalable and reproducible SLAMseq data analysis. Diagnostic plotting features and our MultiQC plugin will make your SLAMseq data ready for immediate QA and interpretation.
  3 KB (294 words) - 20:55, 27 May 2022
• Osprey
  ...and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data. ...Processing, Reconstruction & Estimation of Magnetic Resonance Spectroscopy Data. J Neurosci Meth 343:108827 (2020).]
  2 KB (280 words) - 18:01, 19 August 2022
• Imoka
  iMOKA is a software that enables a comprehensive analysis of sequencing data indexing, iMOKA can easily integrate data from multiple experiments and also
  3 KB (346 words) - 17:07, 27 May 2022
• DeepTools
  ...ing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard ...Manke T. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research. 2016 Apr 13:gkw257.]
  3 KB (360 words) - 14:35, 15 August 2022
• HOMER
  ...DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. ...ng findMotifsGenome.pl to store the pre-parsed genome files locally as the data/genomes/*/preparsed/ are not writable by users.
  3 KB (330 words) - 18:19, 15 August 2022
• Ngscheckmate
  ...ion before further downstream analysis. Currently, it works only for human data.
  3 KB (390 words) - 18:12, 27 May 2022
• EXpress
  expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on
  3 KB (383 words) - 18:53, 12 August 2022
• NLP
  [[Category:Software]][[Category:Machine Learning]][[Category:Data Science]][[Category:Help]] ...iomedical NLP tasks, featuring advanced models for tasks like medical text analysis, drug interaction extraction, and patient information processing. It also a
  8 KB (1,126 words) - 19:55, 14 May 2024
• SNP-Pipeline
  ...the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety. ...tomated method for constructing SNP matrices from next-generation sequence data. PeerJ Computer Science 1:e20 https://doi.org/10.7717/peerj-cs.20]
  3 KB (306 words) - 17:00, 10 June 2022
• SLAW
  Scalable LC-MS Analysis Workflow slaw /data/apps/tests/slaw/test_input /data/apps/tests/slaw/test_output
  3 KB (389 words) - 23:49, 21 August 2022
• SortMeRNA
  ...he main application of SortMeRNA is filtering rRNA from metatranscriptomic data. ...MeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data", Bioinformatics (2012), doi: 10.1093/bioinformatics/bts611.]
  3 KB (299 words) - 17:00, 10 June 2022
• ParaView
  [[Category:Software]][[Category:Data Science]] ...s to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaV
  3 KB (416 words) - 21:28, 13 October 2023
• Hail
  ...a science tools that can be used to interrogate even biobank-scale genomic data (e.g. UK Biobank, gnomAD, TopMed, FinnGen, and Biobank Japan).
  3 KB (353 words) - 17:42, 19 October 2021
• Galaxy
  ...resources for running jobs, transparent user account access and convenient data upload, as well as full system and user support by the RC staff. ...l.edu UFRC Support Ticket System] to request adding new tools or reference data to the Galaxy and to file problem reports. '''Note: If you are submitting a
  4 KB (562 words) - 18:05, 9 November 2022
• V-pipe
  ...pe is a workflow designed for analysis of next generation sequencing (NGS) data from viral pathogens. It produces a number of results in a curated format. ...line for assessing viral genetic diversity from high-throughput sequencing data." Bioinformatics, January. doi:10.1093/bioinformatics/btab015.
  3 KB (296 words) - 17:20, 22 August 2022
• Rsync
  [[Category:Transfer Data]] ...een two computer systems. UFRC now provides a URL for users to rsync their data to and from the cluster. The basic syntax of the rsync command is:
  3 KB (506 words) - 21:25, 28 July 2023
• Popoolation
  ...greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.
  3 KB (321 words) - 21:23, 6 December 2019

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