Search results

• Whiteboxtools
  ...n package; instead it is meant to serve as an analytical backend for other data visualization software, mainly GIS.
  3 KB (408 words) - 17:43, 22 August 2022
• METAL
  ...no loss of efficiency compared to analysis of a combined dataset including data from all individual studies. * HPC_{{uc:{{#var:app}}}}_EX - example data directory
  3 KB (426 words) - 19:27, 18 August 2022
• ProbABEL
  Genome-wide association analysis of imputed data. ...t for association in samples with differential relationships, facilitating analysis in family-based studies, studies performed in human genetically isolated po
  3 KB (371 words) - 19:35, 21 August 2022
• MAGMA-GWAS
  ...genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.
  2 KB (273 words) - 19:35, 23 February 2021
• SOLAR
  ...al features include functionality for mega and meta-genetic analyses where data from diverse cohorts can be pooled to improve statistical significance.
  3 KB (328 words) - 21:24, 6 December 2019
• Ydata-profiling
  ...iling delivers an extended analysis of a DataFrame while allowing the data analysis to be exported in different formats such as html and json.
  2 KB (280 words) - 19:05, 1 December 2023
• Mvftools
  ...ogenetic and population genetic analyses, and small file sizes that enable data sharing and distribution. ...lore.ieee.org/document/7360178 Pease JB and BK Rosenzweig. 2018. "Encoding Data Using Biological Principles: the Multisample Variant Format for Phylogenomi
  3 KB (370 words) - 13:58, 30 April 2020
• Bxh xcede tools
  ...s of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts.
  2 KB (291 words) - 18:22, 12 August 2022
• GUAVA
  ...we believe that GUAVA is a powerful and time saving tool for ATAC-seq data analysis. The GUAVA setup contains a script to configure and install dependencies wh
  3 KB (351 words) - 21:20, 6 December 2019
• MetaWRAP
  ...m, which means you can use only the modules you are interested in for your data. ...ation: MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis. If certain software wrapped into metaWRAP were integral to your investigat
  3 KB (412 words) - 22:31, 8 September 2020
• Ferret
  ...gory: Geospatial]][[Category:Climate]][[Category:Visualization]][[Category:Data Science]] ...riables may be defined interactively as mathematical expressions involving data set variables. Calculations may be applied over arbitrarily shaped regions.
  3 KB (359 words) - 20:26, 24 August 2022
• AltAnalyze
  ...icing graph). AltAnalyze is compatible with various data inputs for RNASeq data (FASTQ, BAM, BED), microarray platforms (Gene 1.0, Exon 1.0, junction and 3
  3 KB (398 words) - 19:14, 10 June 2022
• ANGSD
  ...is on called genotypes. This is especially useful for low and medium depth data. The software is written in C++ and has been used on large sample sizes. ...r manipulating '.bam' files, but solely a tool to perform various kinds of analysis. We recommend the excellent program SAMtools for outputting and modifying b
  3 KB (355 words) - 12:42, 12 August 2022
• TASSEL
  TASSEL stands for Trait Analysis by aSSociation, Evolution and Linkage. Its primary function continues to be ...rincipal component analysis, cluster analysis, missing data imputation and data visualization.  TASSEL development has been led by a group focused on maiz
  3 KB (386 words) - 16:13, 22 August 2022
• Mailing Lists
  ...o this list. Discussion about any aspects of biological computing and data analysis is also welcome.
  778 bytes (110 words) - 20:34, 2 August 2021
• BatMeth2
  In order to complete the DNA methylation data analysis more conveniently, for DNA methylation analysis. During the execution of BatMeth2 Tool, an
  3 KB (324 words) - 18:57, 17 September 2021
• VAMPIR
  [[Category:Software]][[Category:Performance Analysis]] ...able fast and interactive rendering of very complex performance monitoring data.
  3 KB (321 words) - 17:22, 22 August 2022
• ROOT
  [[Category:Software]][[Category:Data Science]] ...al parallel processing framework, PROOF, that can considerably speed up an analysis.
  3 KB (358 words) - 16:48, 21 August 2022
• SplAdder
  ...he alignment data. The quantified events can then be used for differential analysis.
  3 KB (304 words) - 15:50, 22 August 2022
• S.A.G.E
  S.A.G.E. (Statistical Analysis for Genetic Epidemiology) ...rograms for use in the genetic analysis of family, pedigree and individual data.
  2 KB (277 words) - 15:17, 10 September 2021
• Mosaic
  ...nient handling and visualization of single-cell data to enable exploratory analysis.
  2 KB (282 words) - 14:15, 14 October 2021
• ClonalFrame
  ClonalFrame can be applied to any kind of sequence data, from a fragment of DNA to whole genomes. It is well suited for the analysis of MLST
  3 KB (349 words) - 18:33, 12 August 2022
• MOABS
  ...cient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing. ...le and differential methylation for multiple samples, and other downstream analysis.
  2 KB (291 words) - 19:53, 12 August 2022
• SeqyClean
  ...ary preparation. Such nucleotides can potentially case hurdles during data analysis and hereby need to be removed. In additional, the noise, which is presented
  3 KB (312 words) - 22:41, 21 August 2022
• AFNI
  ...C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It should be used for resea RW Cox. AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages. Computers a
  3 KB (363 words) - 20:52, 11 August 2022
• QAPA
  Analysis of alternative polyadenylation (APA) from RNA-seq data (human and mouse). QAPA consists of two main components: ...od for the systematic analysis of alternative polyadenylation from RNA-seq data. Genome Biol. 19, 45.]
  3 KB (305 words) - 16:54, 15 January 2021
• Nsight
  ...egory:Software]][[Category:Utility]][[Category:GPU]][[Category:Performance Analysis]] ...based analysis scripts for post-processing results. The rules-based guided analysis helps isolate and fix memory throughput, compute, and occupancy inefficienc
  3 KB (316 words) - 20:39, 24 August 2022
• FSL
  ...omprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. ..., C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009
  3 KB (365 words) - 16:47, 17 January 2023
• ETE3
  ...c analysis, it can also be used to deal with clustering trees or any other data that can be represented as a hierarchical tree. ...v.msw046 ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Jaime Huerta-Cepas, Francois Serra and Peer Bork. Mol Biol Evol 2016; doi:
  3 KB (400 words) - 19:13, 10 June 2022
• SPM
  ...ded statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM. ...time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.
  3 KB (327 words) - 17:00, 13 February 2024
• Nimare
  ...for performing meta-analyses, and derivative analyses using meta-analytic data, of the neuroimaging literature. While meta-analytic packages exist which i ...ng (MACM) analysis, peaks2maps image reconstruction, and contrast map meta-analysis. '''Each workflow should generate a boilerplate paragraph with details abou
  3 KB (343 words) - 15:27, 15 August 2022
• TrackVis/DTK
  TrackVis is a software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography. Features of ...ormat of the track data file allowing users to integrate customized scalar data into the track file and visualize and analyze it. Save and restore scenes i
  3 KB (418 words) - 14:56, 18 October 2022
• Methylpy
  Methylpy, a pyhton-based analysis pipeline for (single-cell) (whole-genome) bisulfite sequencing data
  3 KB (309 words) - 21:21, 6 December 2019
• NONMEM
  ...effects modelling tool used in population pharmacokinetic/pharmacodynamic analysis. ...in previous versions. NONMEM® can be used to simulate data as well as fit data.
  3 KB (439 words) - 21:23, 6 December 2019
• Ovito
  * automate simulation post-processing, visualization, and data analysis tasks, * integrate OVITO’s file I/O, data analysis, and rendering capabilities into custom workflows and external Python progr
  3 KB (333 words) - 15:29, 1 December 2023
• Cytoscape
  ...e core distribution provides a basic set of features for data integration, analysis, and visualization.
  3 KB (334 words) - 14:23, 15 August 2022
• Garfield
  ...y or functional annotations (primarily from ENCODE and Roadmap epigenomics data) to find features relevant to a phenotype of interest. ...0K Consortium, Ian Dunham, Ewan Birney and Nicole Soranzo. GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction. doi:
  3 KB (342 words) - 22:51, 30 November 2022
• MEGAN
  ...Nalyzer) is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools * Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA
  3 KB (338 words) - 15:38, 15 April 2024
• Plink
  PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a co ...(e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for
  3 KB (342 words) - 20:25, 12 August 2022
• MitoPhAST
  ...tics bottleneck in preparing and utilising such data for phylogenetic data analysis. We present, MitoPhAST, an automated tool that: ...ncorporates nuclear gene sequences (if supplied by user) into phylogenetic analysis.
  3 KB (382 words) - 14:27, 23 April 2020
• EQTLA
  ...orming both cis- and trans-eQTL analysis given a set of raw genetic marker data and expression values.
  2 KB (269 words) - 18:52, 12 August 2022
• QIIME2
  ...from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has b
  3 KB (435 words) - 15:15, 19 August 2022
• EEGLAB
  event-related EEG, MEG and other electrophysiological data using independent component analysis (ICA), time/frequency analysis, and other methods
  2 KB (271 words) - 14:56, 15 August 2022
• Gblocks
  prior to phylogenetic analysis. Gblocks selects blocks in a similar way as the final alignment more suitable for phylogenetic analysis. Gblocks outputs
  3 KB (441 words) - 13:56, 13 June 2022
• Rnalysis
  ...and data visualization through clustering analysis and gene-set enrichment analysis. RNAlysis: analyze your RNA sequencing data without writing a single line of code. BMC Biology, 21, 74.
  5 KB (648 words) - 16:12, 25 April 2023
• GrADS
  ...two data models for handling gridded and station data. GrADS supports many data file formats, including binary (stream or sequential), GRIB2, NetCDF, and H
  3 KB (334 words) - 20:26, 24 August 2022
• TRANSIT
  ...provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition
  2 KB (279 words) - 21:29, 6 December 2019
• EMBOSS
  ...integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercia
  3 KB (372 words) - 15:01, 15 August 2022
• FAST
  ...astA format). FAST tools expose the power of Perl and BioPerl for sequence analysis to non-programmers in an easy-to-learn command-line paradigm. .../articles/10.3389/fgene.2015.00172/full Lawrence et al. (2015). FAST: FAST Analysis of Sequences Toolbox in Frontiers in Genetics, and Stajich et al. (2002)]
  3 KB (358 words) - 21:21, 6 December 2019
• 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

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