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• 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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