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gwasrapidd - 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

'GWAS' R 'API' Data Download. This package provides easy access to the 'NHGRI'-'EBI' 'GWAS' Catalog data by accessing the 'REST' 'API' <https://www.ebi.ac.uk/gwas/rest/docs/api/>.

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thirdpartyclientbiomedicalinformaticsgenomewideassociationsnpassociation-studiesgwas-cataloghumanrest-clienttraittrait-ontology

8.37 score 103 stars 1 dependents 85 scripts 912 downloads

eunis.habitats - EUNIS Habitat Classification

The EUNIS habitat classification is a comprehensive pan-European system for habitat identification <https://www.eea.europa.eu/data-and-maps/data/eunis-habitat-classification-1>. This is an R data package providing the EUNIS classification system. The classification is hierarchical and covers all types of habitats from natural to artificial, from terrestrial to freshwater and marine. The habitat types are identified by specific codes, names and descriptions and come with schema crosswalks to other habitat typologies.

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eunishabitat

3.48 score 6 stars 7 scripts 177 downloads

quincunx - REST API Client for the 'PGS' Catalog

Programmatic access to the 'PGS' Catalog. This package provides easy access to 'PGS' Catalog data by accessing the REST API <https://www.pgscatalog.org/rest/>.

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gwaspolygenic-risk-scorespolygenic-scores

2.98 score 8 stars 24 scripts 102 downloads

wig - Import WIG Data into R in Long Format

Import WIG data into R in long format.

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3.48 score 8 scripts 222 downloads

ruijter - Technical Data Sets by Ruijter et al. (2013)

The real-time quantitative polymerase chain reaction (qPCR) technical data sets by Ruijter et al. (2013) <doi:10.1016/j.ymeth.2012.08.011>: (i) the four-point 10-fold dilution series; (ii) 380 replicates; and (iii) the competimer data set. These three data sets can be used to benchmark qPCR methods. Original data set is available at <https://medischebiologie.nl/wp-content/uploads/2019/02/qpcrdatamethods.zip>. This package fixes incorrect annotations in the original data sets.

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qpcr

3.18 score 3 stars 1 scripts 656 downloads

vermeulen - Biomarker Data Set by Vermeulen et al. (2009)

The biomarker data set by Vermeulen et al. (2009) <doi:10.1016/S1470-2045(09)70154-8> is provided. The data source, however, is by Ruijter et al. (2013) <doi:10.1016/j.ymeth.2012.08.011>. The original data set may be downloaded from <https://medischebiologie.nl/wp-content/uploads/2019/02/qpcrdatamethods.zip>. This data set is for a real-time quantitative polymerase chain reaction (PCR) experiment that comprises the raw fluorescence data of 24,576 amplification curves. This data set comprises 59 genes of interest and 5 reference genes. Each gene was assessed on 366 neuroblastoma complementary DNA (cDNA) samples and on 18 standard dilution series samples (10-fold 5-point dilution series x 3 replicates + no template controls (NTC) x 3 replicates).

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qpcrqpcr-analysis

3.18 score 3 stars 2 scripts 637 downloads

agvgd - An R Implementation of the 'Align-GVGD' Method

'Align-GVGD' ('A-GVGD') is a method to predict the impact of 'missense' substitutions based on the properties of amino acid side chains and protein multiple sequence alignments <doi:10.1136/jmg.2005.033878>. 'A-GVGD' is an extension of the original 'Grantham' distance to multiple sequence alignments. This package provides an alternative R implementation to the web version found on <http://agvgd.hci.utah.edu/>.

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3.18 score 3 stars 6 scripts 272 downloads

batsch - Real-Time PCR Data Sets by Batsch et al. (2008)

Real-time quantitative polymerase chain reaction (qPCR) data sets by Batsch et al. (2008) <doi:10.1186/1471-2105-9-95>. This package provides five data sets, one for each PCR target: (i) rat SLC6A14, (ii) human SLC22A13, (iii) pig EMT, (iv) chicken ETT, and (v) human GAPDH. Each data set comprises a five-point, four-fold dilution series. For each concentration there are three replicates. Each amplification curve is 45 cycles long. Original raw data file: <https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-9-95/MediaObjects/12859_2007_2080_MOESM5_ESM.xls>.

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qpcr

2.70 score 1 stars 1 scripts 692 downloads

rutledge - Real-Time PCR Data Sets by Rutledge et al. (2004)

Real-time quantitative polymerase chain reaction (qPCR) data by Rutledge et al. (2004) <doi:10.1093/nar/gnh177> in tidy format. The data comprises a six-point, ten-fold dilution series, repeated in five independent runs, for two different amplicons. In each run, each standard concentration is replicated four times. For the original raw data file see the Supplementary Data section: <https://academic.oup.com/nar/article/32/22/e178/2375678#supplementary-data>.

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2.70 score 1 stars 1 scripts 640 downloads

guescini - Real-Time PCR Data Sets by Guescini et al. (2008)

Real-time quantitative polymerase chain reaction (qPCR) data by Guescini et al. (2008) <doi:10.1186/1471-2105-9-326> in tidy format. This package provides two data sets where the amplification efficiency has been modulated: either by changing the amplification mix concentration, or by increasing the concentration of IgG, a PCR inhibitor. Original raw data files: <https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-9-326/MediaObjects/12859_2008_2311_MOESM1_ESM.xls> and <https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-9-326/MediaObjects/12859_2008_2311_MOESM5_ESM.xls>.

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2.70 score 1 stars 174 downloads

grantham - Calculate the 'Grantham' Distance

A minimal set of routines to calculate the 'Grantham' distance <doi:10.1126/science.185.4154.862>. The 'Grantham' distance attempts to provide a proxy for the evolutionary distance between two amino acids based on three key chemical properties: composition, polarity and molecular volume. In turn, evolutionary distance is used as a proxy for the impact of missense mutations. The higher the distance, the more deleterious the substitution is expected to be.

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2.65 score 3 stars 1 dependents 9 scripts 649 downloads

dataset.json.examples - Dataset-JSON Example Files

An R data package providing a set of Dataset-JSON files comprising SDTM and ADaM datasets. Examples are originally from: <https://github.com/cdisc-org/DataExchange-DatasetJson>.

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1.70 score 1 stars 2 scripts

protean - Sequence Profiles of OncoKB Genes

A data package of sequence profiles of OncoKB genes. These profiles are obtained via Ensembl's REST API and derived from the pairwise alignment of the human sequence with its orthologs.

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1.70 score 4 scripts

geisha - GEISHA Expression Data

GEISHA expression data. These data are obtained from GEISHA <http://geisha.arizona.edu/geisha/downloads.jsp/>.

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1.70 score 1 stars