MHCtools (Q63227): Difference between revisions

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Property / last update
22 March 2023
Timestamp+2023-03-22T00:00:00Z
Timezone+00:00
CalendarGregorian
Precision1 day
Before0
After0
 
Property / last update: 22 March 2023 / rank
Normal rank
 
Property / imports
 
Property / imports: graphics / rank
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Property / imports
 
Property / imports: openxlsx / rank
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Property / software version identifier
 
1.0.0
Property / software version identifier: 1.0.0 / rank
 
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Property / software version identifier: 1.0.0 / qualifier
 
publication date: 29 September 2017
Timestamp+2017-09-29T00:00:00Z
Timezone+00:00
CalendarGregorian
Precision1 day
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After0
Property / software version identifier
 
1.1.0
Property / software version identifier: 1.1.0 / rank
 
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Property / software version identifier: 1.1.0 / qualifier
 
publication date: 23 October 2017
Timestamp+2017-10-23T00:00:00Z
Timezone+00:00
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Precision1 day
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After0
Property / software version identifier
 
1.1.1
Property / software version identifier: 1.1.1 / rank
 
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Property / software version identifier: 1.1.1 / qualifier
 
publication date: 4 February 2019
Timestamp+2019-02-04T00:00:00Z
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Precision1 day
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Property / software version identifier
 
1.2.0
Property / software version identifier: 1.2.0 / rank
 
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Property / software version identifier: 1.2.0 / qualifier
 
publication date: 8 August 2019
Timestamp+2019-08-08T00:00:00Z
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Precision1 day
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Property / software version identifier
 
1.2.1
Property / software version identifier: 1.2.1 / rank
 
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Property / software version identifier: 1.2.1 / qualifier
 
publication date: 11 August 2019
Timestamp+2019-08-11T00:00:00Z
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Precision1 day
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Property / software version identifier
 
1.3.0
Property / software version identifier: 1.3.0 / rank
 
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Property / software version identifier: 1.3.0 / qualifier
 
publication date: 16 September 2020
Timestamp+2020-09-16T00:00:00Z
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Precision1 day
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1.4.0
Property / software version identifier: 1.4.0 / rank
 
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Property / software version identifier: 1.4.0 / qualifier
 
publication date: 14 September 2021
Timestamp+2021-09-14T00:00:00Z
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Precision1 day
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Property / software version identifier
 
1.4.1
Property / software version identifier: 1.4.1 / rank
 
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Property / software version identifier: 1.4.1 / qualifier
 
publication date: 11 October 2021
Timestamp+2021-10-11T00:00:00Z
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Precision1 day
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Property / software version identifier
 
1.4.2
Property / software version identifier: 1.4.2 / rank
 
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Property / software version identifier: 1.4.2 / qualifier
 
publication date: 23 May 2022
Timestamp+2022-05-23T00:00:00Z
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Property / software version identifier
 
1.4.3
Property / software version identifier: 1.4.3 / rank
 
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Property / software version identifier: 1.4.3 / qualifier
 
publication date: 15 August 2022
Timestamp+2022-08-15T00:00:00Z
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1.5.0
Property / software version identifier: 1.5.0 / rank
 
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Property / software version identifier: 1.5.0 / qualifier
 
publication date: 19 October 2022
Timestamp+2022-10-19T00:00:00Z
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Precision1 day
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Property / software version identifier
 
1.5.2
Property / software version identifier: 1.5.2 / rank
 
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Property / software version identifier: 1.5.2 / qualifier
 
publication date: 1 July 2023
Timestamp+2023-07-01T00:00:00Z
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Precision1 day
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Property / software version identifier
 
1.5.3
Property / software version identifier: 1.5.3 / rank
 
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Property / software version identifier: 1.5.3 / qualifier
 
publication date: 8 July 2023
Timestamp+2023-07-08T00:00:00Z
Timezone+00:00
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Precision1 day
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Property / last update
 
8 July 2023
Timestamp+2023-07-08T00:00:00Z
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Precision1 day
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Property / last update: 8 July 2023 / rank
 
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Property / description
 
Fifteen tools for bioinformatics processing and analysis of major histocompatibility complex (MHC) data. The functions are tailored for amplicon data sets that have been filtered using the dada2 method (for more information on dada2, visit <https://benjjneb.github.io/dada2/> ), but even other types of data sets can be analyzed. The ReplMatch() function matches replicates in data sets in order to evaluate genotyping success. The GetReplTable() and GetReplStats() functions perform such an evaluation. The CreateFas() function creates a fasta file with all the sequences in the data set. The CreateSamplesFas() function creates individual fasta files for each sample in the data set. The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise comparisons of all sequences in a data set, and mean distances of all pairwise comparisons within each sample in a data set. The function additionally outputs five tables with physico-chemical z-descriptor values (based on Sandberg et al. 1998) for each amino acid position in all sequences in the data set. These tables may be useful for further downstream analyses, such as estimation of MHC supertypes. The BootKmeans() function is a wrapper for the kmeans() function of the 'stats' package, which allows for bootstrapping. Bootstrapping k-estimates may be desirable in data sets, where e.g. BIC- vs. k-values do not produce clear inflection points ("elbows"). BootKmeans() performs multiple runs of kmeans() and estimates optimal k-values based on a user-defined threshold of BIC reduction. The method is an automated and bootstrapped version of visually inspecting elbow plots of BIC- vs. k-values. The ClusterMatch() function is a tool for evaluating whether different k-means() clustering models identify similar clusters, and summarize bootstrap model stats as means for different estimated values of k. It is designed to take files produced by the BootKmeans() function as input, but other data can be analysed if the descriptions of the required data formats are observed carefully. The PapaDiv() function compares parent pairs in the data set and calculate their joint MHC diversity, taking into account sequence variants that occur in both parents. The HpltFind() function infers putative haplotypes from families in the data set. The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of the haplotype inference. The CreateHpltOccTable() function creates a binary (logical) haplotype-sequence occurrence matrix from the output of HpltFind(), for easy overview of which sequences are present in which haplotypes. The HpltMatch() function compares haplotypes to help identify overlapping and potentially identical types. The NestTablesXL() function translates the output from HpltFind() to an Excel workbook, that provides a convenient overview for evaluation and curating of the inferred putative haplotypes.
Property / description: Fifteen tools for bioinformatics processing and analysis of major histocompatibility complex (MHC) data. The functions are tailored for amplicon data sets that have been filtered using the dada2 method (for more information on dada2, visit <https://benjjneb.github.io/dada2/> ), but even other types of data sets can be analyzed. The ReplMatch() function matches replicates in data sets in order to evaluate genotyping success. The GetReplTable() and GetReplStats() functions perform such an evaluation. The CreateFas() function creates a fasta file with all the sequences in the data set. The CreateSamplesFas() function creates individual fasta files for each sample in the data set. The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise comparisons of all sequences in a data set, and mean distances of all pairwise comparisons within each sample in a data set. The function additionally outputs five tables with physico-chemical z-descriptor values (based on Sandberg et al. 1998) for each amino acid position in all sequences in the data set. These tables may be useful for further downstream analyses, such as estimation of MHC supertypes. The BootKmeans() function is a wrapper for the kmeans() function of the 'stats' package, which allows for bootstrapping. Bootstrapping k-estimates may be desirable in data sets, where e.g. BIC- vs. k-values do not produce clear inflection points ("elbows"). BootKmeans() performs multiple runs of kmeans() and estimates optimal k-values based on a user-defined threshold of BIC reduction. The method is an automated and bootstrapped version of visually inspecting elbow plots of BIC- vs. k-values. The ClusterMatch() function is a tool for evaluating whether different k-means() clustering models identify similar clusters, and summarize bootstrap model stats as means for different estimated values of k. It is designed to take files produced by the BootKmeans() function as input, but other data can be analysed if the descriptions of the required data formats are observed carefully. The PapaDiv() function compares parent pairs in the data set and calculate their joint MHC diversity, taking into account sequence variants that occur in both parents. The HpltFind() function infers putative haplotypes from families in the data set. The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of the haplotype inference. The CreateHpltOccTable() function creates a binary (logical) haplotype-sequence occurrence matrix from the output of HpltFind(), for easy overview of which sequences are present in which haplotypes. The HpltMatch() function compares haplotypes to help identify overlapping and potentially identical types. The NestTablesXL() function translates the output from HpltFind() to an Excel workbook, that provides a convenient overview for evaluation and curating of the inferred putative haplotypes. / rank
 
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Property / author
 
Property / author: Jacob Roved / rank
 
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Property / copyright license
 
Property / copyright license: MIT license / rank
 
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Property / copyright license
 
Property / copyright license: File License / rank
 
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Property / copyright license: File License / qualifier
 
Property / depends on software
 
Property / depends on software: R / rank
 
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Property / depends on software: R / qualifier
 
Property / imports
 
Property / imports: stats / rank
 
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Property / imports: utils / rank
 
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Property / imports: mgcv / rank
 
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Property / imports: grDevices / rank
 
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Property / imports: graphics / rank
 
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Property / imports: openxlsx / rank
 
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Property / MaRDI profile type
 
Property / MaRDI profile type: MaRDI software profile / rank
 
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links / mardi / namelinks / mardi / name
 

Latest revision as of 18:56, 12 March 2024

Analysis of MHC Data in Non-Model Species
Language Label Description Also known as
English
MHCtools
Analysis of MHC Data in Non-Model Species

    Statements

    1.5.1
    22 March 2023
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    1.0.0
    29 September 2017
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    1.1.0
    23 October 2017
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    1.1.1
    4 February 2019
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    1.2.0
    8 August 2019
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    1.2.1
    11 August 2019
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    1.3.0
    16 September 2020
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    1.4.0
    14 September 2021
    0 references
    1.4.1
    11 October 2021
    0 references
    1.4.2
    23 May 2022
    0 references
    1.4.3
    15 August 2022
    0 references
    1.5.0
    19 October 2022
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    1.5.2
    1 July 2023
    0 references
    1.5.3
    8 July 2023
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    8 July 2023
    0 references
    Fifteen tools for bioinformatics processing and analysis of major histocompatibility complex (MHC) data. The functions are tailored for amplicon data sets that have been filtered using the dada2 method (for more information on dada2, visit <https://benjjneb.github.io/dada2/> ), but even other types of data sets can be analyzed. The ReplMatch() function matches replicates in data sets in order to evaluate genotyping success. The GetReplTable() and GetReplStats() functions perform such an evaluation. The CreateFas() function creates a fasta file with all the sequences in the data set. The CreateSamplesFas() function creates individual fasta files for each sample in the data set. The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise comparisons of all sequences in a data set, and mean distances of all pairwise comparisons within each sample in a data set. The function additionally outputs five tables with physico-chemical z-descriptor values (based on Sandberg et al. 1998) for each amino acid position in all sequences in the data set. These tables may be useful for further downstream analyses, such as estimation of MHC supertypes. The BootKmeans() function is a wrapper for the kmeans() function of the 'stats' package, which allows for bootstrapping. Bootstrapping k-estimates may be desirable in data sets, where e.g. BIC- vs. k-values do not produce clear inflection points ("elbows"). BootKmeans() performs multiple runs of kmeans() and estimates optimal k-values based on a user-defined threshold of BIC reduction. The method is an automated and bootstrapped version of visually inspecting elbow plots of BIC- vs. k-values. The ClusterMatch() function is a tool for evaluating whether different k-means() clustering models identify similar clusters, and summarize bootstrap model stats as means for different estimated values of k. It is designed to take files produced by the BootKmeans() function as input, but other data can be analysed if the descriptions of the required data formats are observed carefully. The PapaDiv() function compares parent pairs in the data set and calculate their joint MHC diversity, taking into account sequence variants that occur in both parents. The HpltFind() function infers putative haplotypes from families in the data set. The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of the haplotype inference. The CreateHpltOccTable() function creates a binary (logical) haplotype-sequence occurrence matrix from the output of HpltFind(), for easy overview of which sequences are present in which haplotypes. The HpltMatch() function compares haplotypes to help identify overlapping and potentially identical types. The NestTablesXL() function translates the output from HpltFind() to an Excel workbook, that provides a convenient overview for evaluation and curating of the inferred putative haplotypes.
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    Identifiers

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