Package VSE. March 21, 2016
|
|
|
- Darlene Claire Walsh
- 5 years ago
- Views:
Transcription
1 Type Package Title Variant Set Enrichment Version 0.99 Date Package VSE March 21, 2016 Author Musaddeque Ahmed Maintainer Hansen He Calculates the enrichment of associated variant set (AVS) for an array of genomic regions. The AVS is the collection of disjoint LD blocks computed from a list of disease associated SNPs and their linked (LD) SNPs. VSE generates a null distribution of matched random variant sets (MRVSs) from 1000 Genome Project Phase III data that are identical to AVS, LD block by block. It then computes the enrichment of AVS intersecting with user provided genomic features (e.g., histone marks or transcription factor binding sites) compared with the null distribution. License GPL-3 LazyData TRUE RoxygenNote Depends GenomicRanges Suggests knitr, rmarkdown, ggplot2 Imports igraph, car, IRanges, parallel VignetteBuilder knitr NeedsCompilation no Repository CRAN Date/Publication :10:53 R topics documented: avssize bedtogranges intersectmatrix loadld
2 2 bedtogranges loadsampleregions makeavs makemrvs variantsetenrichment VSEplot VSEqq VSESummary Index 9 avssize avssize This function will output a dataframe of LD size of each tag SNP avssize(avs) avs A GRanges object which is outputted by loadld function ld<-loadld(file.path(system.file("extdata", "ld_bca_raggr.csv", package="vse")), type="raggr") avs<-makeavs(ld) avssize(avs) bedtogranges bedtogranges This function will convert a bed to GRanges object bedtogranges(file) file A bed file. Must contain at least three columns: chr, start and end.
3 intersectmatrix 3 bedtogranges(file) intersectmatrix intersectmatrix This function will count the intersection tally of AVS and genomic regions intersectmatrix(avs, regions,...) avs regions A GRanges object which is outputted by loadld function A data frame. The data frame contains sample sheet identical to DiffBind or ChIPQC input sample sheets... Heatmap arguments intersectmatrix(avs, regions=samples, col=c("white","grey10"), scale="none", margins=c(10,5), cexrow = 1, cexcol = 0.5, Rowv=NA, Colv=NA)
4 4 loadsampleregions loadld loadld This function will load a raggr output csv or user defined bed file to GRanges object. It is recommended to generate a LD file using If you prefer to use other softwares to calculate LD SNPs (e.g., plink), please format the output to bed files. Please make sure that you use a cutoff of 0.8 for r2 value. loadld(data, type) data type An input file. Must be a raggr generated csv file or a bed file. If a bed file, it must contain at least five columns: chr, start, end, LD_snp_id, tag_snp_id. The type of input file. Must be "bed" or "raggr". ld<-loadld(file.path(system.file("extdata", "ld_bca_raggr.csv", package="vse")), type="raggr") loadsampleregions loadsampleregions Details Value The sample bed files are DNAse-seq, ChIP-seq for H3K4me1, H3K4me3, H3K27ac, H3K27me3 and H3K36me3 for MCF7 cells. The data are obtained from ENCODE project. There is also one samplesheet.csv which is the sample sheet for the bed regions in the format similar to ChIPQC or DiffBind requirement. loadsampleregions() This function will download sample bed files from in /VSE_samples A directory names VSE_samples that will contain 6 bed files and 1 samplesheet.csv
5 makeavs 5 loadsampleregions() makeavs makeavs This function will create disjoint LD blocks from a GRanges object makeavs(x) x A GRanges object which is outputted by loadld function ld<-loadld(file.path(system.file("extdata", "ld_bca_raggr.csv", package="vse")), type="raggr") avs<-makeavs(ld) makemrvs makemrvs This function will calculate matching random variant sets (MRVS) idential to AVS makemrvs(avs, bgsize = 100, mc.cores = 6) avs A GRanges object which is outputted by makeavs function bgsize An integer for the number of MRVS. Default: 100 mc.cores Number of cores to use. Default: 8
6 6 variantsetenrichment ld <- loadld("ld.csv", type="raggr") avs <- makeavs(ld) makemrvs(avs, bgsize=100, mc.cores=8) #As an example, we have added MRVS (size=200) for Breast Cancer AVS. load(file.path(system.file("extdata", "bca.mrvs.200.rda", package="vse"))) variantsetenrichment variantsetenrichment This function will calculate matching random variant sets (MRVS) idential to AVS variantsetenrichment(avs, mrvs, regions) avs mrvs regions A GRangesList object which is outputted by makeavs function A list of GRangesList objects outputted by makemrvs function A data frame. The data frame contains sample sheet identical to DiffBind or ChIPQC input sample sheets variantsetenrichment(avs, mrvs, regions=samples) #We have included the output from our example analysis with the package. \ You can load the example VariantSetEnrichment output by typing: load(file.path(system.file("extdata", "vse_output.rda", package="vse")))
7 VSEplot 7 VSEplot VSEplot This function will generate a figure for VSE analysis VSEplot(data, padj = 0.01,...) data A list of matrices outputted by the function VariantSetEnrichment padj Bonferroni adjusted p-value cutoff. Default: from boxplot #Load pre-saved object "bca.vse" as an example VSE output load(file.path(system.file("extdata", "vse_output.rda", package="vse"))) VSEplot(bca.vse, las=2,pch=20, cex=1, cex.main=0.6, padj=0.05) VSEqq VSEqq This function will generate QQ plots of normal distribution VSEqq(data,...) data A matrix outputted by the function VariantSetEnrichment... for qqnorm plot #Load pre-saved object "bca.vse" as an example VSE output load(file.path(system.file("extdata", "vse_output.rda", package="vse"))) VSEqq(bca.vse)
8 8 VSESummary VSESummary VSESummary This function will compute the enrichment from a VSE matrix VSESummary(data) data A matrix outputted by the function VariantSetEnrichment #Load pre-saved object "bca.vse" as an example VSE output load(file.path(system.file("extdata", "vse_output.rda", package="vse"))) VSESummary(bca.vse)
9 Index Topic AVS,Granges avssize, 2 intersectmatrix, 3 makeavs, 5 Topic LD,bed,raggr,GRanges loadld, 4 Topic VSE, VSEplot, 7 VSEqq, 7 VSESummary, 8 Topic VSE makemrvs, 5 variantsetenrichment, 6 Topic bed,granges bedtogranges, 2 Topic boxplot VSEplot, 7 VSEqq, 7 Topic enrichment VSESummary, 8 Topic sample,histone,mcf7 loadsampleregions, 4 avssize, 2 bedtogranges, 2 intersectmatrix, 3 loadld, 4 loadsampleregions, 4 makeavs, 5 makemrvs, 5 variantsetenrichment, 6 VSEplot, 7 VSEqq, 7 VSESummary, 8 9
Package bisect. April 16, 2018
Package bisect April 16, 2018 Title Estimating Cell Type Composition from Methylation Sequencing Data Version 0.9.0 Maintainer Eyal Fisher Author Eyal Fisher [aut, cre] An implementation
Package DMCHMM. January 19, 2019
Package DMCHMM January 19, 2019 Type Package Title Differentially Methylated CpG using Hidden Markov Model Version 1.4.0 Author Farhad Shokoohi Maintainer A pipeline for identifying differentially methylated
Package ECctmc. May 1, 2018
Type Package Package ECctmc May 1, 2018 Title Simulation from Endpoint-Conditioned Continuous Time Markov Chains Version 0.2.5 Date 2018-04-30 URL https://github.com/fintzij/ecctmc BugReports https://github.com/fintzij/ecctmc/issues
Package WordR. September 7, 2017
Type Package Package WordR September 7, 2017 Title Rendering Word Documents with R Inline Code Version 0.2.2 Author Tomas Hovorka Maintainer Tomas Hovorka Serves for rendering
Package cattonum. R topics documented: May 2, Type Package Version Title Encode Categorical Features
Type Package Version 0.0.2 Title Encode Categorical Features Package cattonum May 2, 2018 Functions for dummy encoding, frequency encoding, label encoding, leave-one-out encoding, mean encoding, median
Package SEMrushR. November 3, 2018
Type Package Title R Interface to Access the 'SEMrush' API Version 0.1.0 Package SEMrushR November 3, 2018 Implements methods for querying SEO (Search Engine Optimization) and SEM (Search Engine Marketing)
Package datasets.load
Title Interface for Loading Datasets Version 0.1.0 Package datasets.load December 14, 2016 Visual interface for loading datasets in RStudio from insted (unloaded) s. Depends R (>= 3.0.0) Imports shiny,
Package fastdummies. January 8, 2018
Type Package Package fastdummies January 8, 2018 Title Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables Version 1.0.0 Description Creates dummy columns from columns that have
Package seqcat. March 25, 2019
Package seqcat March 25, 2019 Title High Throughput Sequencing Cell Authentication Toolkit Version 1.4.1 The seqcat package uses variant calling data (in the form of VCF files) from high throughput sequencing
Package cregulome. September 13, 2018
Type Package Version 0.2.0 Package cregulome September 13, 2018 Title Obtain and Visualize Regulome-Gene Expression Correlations in Cancer Builds a 'SQLite' database file of pre-calculated transcription
Package CatEncoders. March 8, 2017
Type Package Title Encoders for Categorical Variables Version 0.1.1 Author nl zhang Package CatEncoders Maintainer nl zhang March 8, 2017 Contains some commonly used categorical
Package barcoder. October 26, 2018
Package barcoder October 26, 2018 Title Labelling, Tracking, and Collecting Data from Biological Samples Version 0.1.0 Maintainer Robert Colautti Tools to generate unique identifiers
Package canvasxpress
Version 1.18.2 Package canvasxpress Title Visualization Package for CanvasXpress in R January 19, 2018 Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone
Package FunciSNP. November 16, 2018
Type Package Package FunciSNP November 16, 2018 Title Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs Version 1.26.0 Date 2013-01-19 Author
Package rsppfp. November 20, 2018
Package rsppfp November 20, 2018 Title R's Shortest Path Problem with Forbidden Subpaths Version 1.0.3 Maintainer Melina Vidoni An implementation of functionalities
Package PDN. November 4, 2017
Type Package Title Personalized Disease Network Version 0.1.0 Package PDN November 4, 2017 Author Javier Cabrera , Fei Wang Maintainer Zhenbang Wang
Package metagene. November 1, 2018
Version 2.15.0 Date 2017-10-13 Title A package to produce metagene plots Author Charles Joly Beauparlant Package metagene November 1, 2018 , Fabien Claude Lamaze
Package geojsonsf. R topics documented: January 11, Type Package Title GeoJSON to Simple Feature Converter Version 1.3.
Type Package Title GeoJSON to Simple Feature Converter Version 1.3.0 Date 2019-01-11 Package geojsonsf January 11, 2019 Converts Between GeoJSON and simple feature objects. License GPL-3 Encoding UTF-8
Package PlasmaMutationDetector
Type Package Package PlasmaMutationDetector Title Tumor Mutation Detection in Plasma Version 1.7.2 Date 2018-05-16 June 11, 2018 Author Yves Rozenholc, Nicolas Pécuchet, Pierre Laurent-Puig Maintainer
Package pairsd3. R topics documented: August 29, Title D3 Scatterplot Matrices Version 0.1.0
Title D3 Scatterplot Matrices Version 0.1.0 Package pairsd3 August 29, 2016 Creates an interactive scatterplot matrix using the D3 JavaScript library. See for more information on D3.
Visualisation, transformations and arithmetic operations for grouped genomic intervals
## Warning: replacing previous import ggplot2::position by BiocGenerics::Position when loading soggi Visualisation, transformations and arithmetic operations for grouped genomic intervals Thomas Carroll
You will be re-directed to the following result page.
ENCODE Element Browser Goal: to navigate the candidate DNA elements predicted by the ENCODE consortium, including gene expression, DNase I hypersensitive sites, TF binding sites, and candidate enhancers/promoters.
Package ChIPseeker. July 12, 2018
Type Package Package ChIPseeker July 12, 2018 Title ChIPseeker for ChIP peak Annotation, Comparison, and Visualization Version 1.16.0 Encoding UTF-8 Maintainer Guangchuang Yu
Package validara. October 19, 2017
Type Package Title Validate Brazilian Administrative Registers Version 0.1.1 Package validara October 19, 2017 Maintainer Gustavo Coelho Contains functions to validate administrative
Package geneslope. October 26, 2016
Type Package Package geneslope October 26, 2016 Title Genome-Wide Association Study with SLOPE Version 0.37.0 Date 2016-10-26 Genome-wide association study (GWAS) performed with SLOPE, short for Sorted
Package sigqc. June 13, 2018
Title Quality Control Metrics for Gene Signatures Version 0.1.20 Package sigqc June 13, 2018 Description Provides gene signature quality control metrics in publication ready plots. Namely, enables the
Package gggenes. R topics documented: November 7, Title Draw Gene Arrow Maps in 'ggplot2' Version 0.3.2
Title Draw Gene Arrow Maps in 'ggplot2' Version 0.3.2 Package gggenes November 7, 2018 Provides a 'ggplot2' geom and helper functions for drawing gene arrow maps. Depends R (>= 3.3.0) Imports grid (>=
Package icnv. R topics documented: March 8, Title Integrated Copy Number Variation detection Version Author Zilu Zhou, Nancy Zhang
Title Integrated Copy Number Variation detection Version 1.2.1 Author Zilu Zhou, Nancy Zhang Package icnv March 8, 2019 Maintainer Zilu Zhou Integrative copy number variation
Package effectr. January 17, 2018
Title Predicts Oomycete Effectors Version 1.0.0 Package effectr January 17, 2018 Predicts cytoplasmic effector proteins using genomic data by searching for motifs of interest using regular expression searches
Package preprosim. July 26, 2016
Package preprosim July 26, 2016 Type Package Title Lightweight Data Quality Simulation for Classification Version 0.2.0 Date 2016-07-26 Data quality simulation can be used to check the robustness of data
Package TrafficBDE. March 1, 2018
Type Package Package TrafficBDE March 1, 2018 Title Traffic Status Prediction in Urban Places using Neural Network Models Version 0.1.0 Date 2018-02-26 Estimate and return either the traffic speed or the
Package lumberjack. R topics documented: July 20, 2018
Package lumberjack July 20, 2018 Maintainer Mark van der Loo License GPL-3 Title Track Changes in Data LazyData no Type Package LazyLoad yes A function composition ('pipe') operator
Package MIRA. October 16, 2018
Version 1.2.0 Date 2018-04-17 Package MIRA October 16, 2018 Title Methylation-Based Inference of Regulatory Activity MIRA measures the degree of ``dip'' in methylation level surrounding a regulatory site
Package multihiccompare
Package multihiccompare September 23, 2018 Title Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available Version 0.99.44 multihiccompare provides
Package haplor. November 1, 2017
Type Package Title Query 'HaploReg' and 'RegulomeDB' Version 1.6.2 Date 2017-10-31 Package haplor November 1, 2017 Maintainer Ilya Y. Zhbannikov A set of utilities for querying
Package gifti. February 1, 2018
Type Package Package gifti February 1, 2018 Title Reads in 'Neuroimaging' 'GIFTI' Files with Geometry Information Version 0.7.5 Author John Muschelli Maintainer John Muschelli Functions
Package kdtools. April 26, 2018
Type Package Package kdtools April 26, 2018 Title Tools for Working with Multidimensional Data Version 0.3.1 Provides various tools for working with multidimensional data in R and C++, including etremely
Package gtrendsr. October 19, 2017
Type Package Title Perform and Display Google Trends Queries Version 1.4.0 Date 2017-10-19 Package gtrendsr October 19, 2017 An interface for retrieving and displaying the information returned online by
Package snplist. December 11, 2017
Type Package Title Tools to Create Gene Sets Version 0.18.1 Date 2017-12-11 Package snplist December 11, 2017 Author Chanhee Yi, Alexander Sibley, and Kouros Owzar Maintainer Alexander Sibley
Package ordinalclust
Type Package Package ordinalclust August 6, 2018 Title Ordinal Data Clustering, Co-Clustering and Classification Version 1.3.1 Date 2018-08-06 Author Margot Selosse, Julien Jacques, Christophe Biernacki
Package shinyfeedback
Type Package Package shinyfeedback August 20, 2018 Title Displays User Feedback Next to Shiny Inputs Version 0.1.0 Date 2018-08-19 Easily display user feedback next to Shiny inputs. The feedback message
Package spark. July 21, 2017
Title 'Sparklines' in the 'R' Terminal Version 2.0.0 Author Gábor Csárdi Package spark July 21, 2017 Maintainer Gábor Csárdi A 'sparkline' is a line chart, without axes and labels.
Package fitbitscraper
Title Scrapes Data from Fitbit Version 0.1.8 Package fitbitscraper April 14, 2017 Author Cory Nissen [aut, cre] Maintainer Cory Nissen Scrapes data from Fitbit
Chromatin signature discovery via histone modification profile alignments Jianrong Wang, Victoria V. Lunyak and I. King Jordan
Supplementary Information for: Chromatin signature discovery via histone modification profile alignments Jianrong Wang, Victoria V. Lunyak and I. King Jordan Contents Instructions for installing and running
Package cooccurnet. January 27, 2017
Type Package Title Co-Occurrence Network Version 0.1.6 Depends R (>= 3.2.0) Package cooccurnet January 27, 2017 Imports seqinr, igraph, bigmemory, Matrix, foreach, parallel, pryr, knitr, doparallel Author
Package calpassapi. August 25, 2018
Title R Interface to Access CalPASS API Version 0.0.1 Package calpassapi August 25, 2018 Description Implements methods for querying data from CalPASS using its API. CalPASS Plus. MMAP API V1. .
Package vinereg. August 10, 2018
Type Package Title D-Vine Quantile Regression Version 0.5.0 Package vinereg August 10, 2018 Maintainer Thomas Nagler Description Implements D-vine quantile regression models with parametric
Package linkspotter. July 22, Type Package
Type Package Package linkspotter July 22, 2018 Title Bivariate Correlations Calculation and Visualization Version 1.2.0 Date 2018-07-18 Compute and visualize using the 'visnetwork' package all the bivariate
Package metaheur. June 30, 2016
Type Package Package metaheur June 30, 2016 Title Metaheuristic Optimization Framework for Preprocessing Combinations Version 0.2.0 Date 2016-6-30 Author Markus Vattulainen Maintainer Markus Vattulainen
Package IsoCorrectoR. R topics documented:
Package IsoCorrectoR March 19, 2019 Title Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments Version 1.0.5 Imports dplyr, magrittr,
Package gpart. November 19, 2018
Package gpart November 19, 2018 Title Human genome partitioning of dense sequencing data by identifying haplotype blocks Version 1.0.0 Depends R (>= 3.5.0), grid, Homo.sapiens, TxDb.Hsapiens.UCSC.hg38.knownGene,
Package scmap. March 29, 2019
Type Package Package scmap March 29, 2019 Title A tool for unsupervised projection of single cell RNA-seq data Version 1.4.1 Author Vladimir Kiselev Maintainer Vladimir Kiselev
Package RTNduals. R topics documented: March 7, Type Package
Type Package Package RTNduals March 7, 2019 Title Analysis of co-regulation and inference of 'dual regulons' Version 1.7.0 Author Vinicius S. Chagas, Clarice S. Groeneveld, Gordon Robertson, Kerstin B.
Package kirby21.base
Type Package Package kirby21.base October 11, 2017 Title Example Data from the Multi-Modal MRI 'Reproducibility' Resource Version 1.6.0 Date 2017-10-10 Author John Muschelli Maintainer
Package dmrseq. September 14, 2018
Type Package Package dmrseq September 14, 2018 Title Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing Version 1.1.15 Author Keegan Korthauer ,
Package ggimage. R topics documented: December 5, Title Use Image in 'ggplot2' Version 0.1.0
Title Use Image in 'ggplot2' Version 0.1.0 Package ggimage December 5, 2017 Supports image files and graphic objects to be visualized in 'ggplot2' graphic system. Depends R (>= 3.3.0), ggplot2 Imports
Package samplesizecmh
Package samplesizecmh Title Power and Sample Size Calculation for the Cochran-Mantel-Haenszel Test Date 2017-12-13 Version 0.0.0 Copyright Spectrum Health, Grand Rapids, MI December 21, 2017 Calculates
Package MetaLonDA. R topics documented: January 22, Type Package
Type Package Package MetaLonDA January 22, 2018 Title Metagenomics Longitudinal Differential Abundance Method Version 1.0.9 Date 2018-1-20 Author Ahmed Metwally, Yang Dai, Patricia Finn, David Perkins
Package climber. R topics documented:
Package climber November 19, 2016 Title Calculate Average Minimal Depth of a Maximal Subtree for 'ranger' Package Forests Version 0.0.1 Calculates first, and second order, average minimal depth of a maximal
Package omu. August 2, 2018
Package omu August 2, 2018 Title A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection Version 1.0.2 Facilitates the creation of intuitive figures to describe metabolomics
Package Hapi. July 28, 2018
Type Package Package Hapi July 28, 2018 Title Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells Version 0.0.3 Author, Han Qu, Jinfeng Chen, Shibo Wang, Le Zhang, Julong
Package GFD. January 4, 2018
Type Package Title Tests for General Factorial Designs Version 0.2.5 Date 2018-01-04 Package GFD January 4, 2018 Author Sarah Friedrich, Frank Konietschke, Markus Pauly Maintainer Sarah Friedrich
Package balance. October 12, 2018
Title Visualize Balances of Compositional Data Version 0.1.6 URL http://github.com/tpq/balance Package balance October 12, 2018 BugReports http://github.com/tpq/balance/issues Balances have become a cornerstone
Package gsalib. R topics documented: February 20, Type Package. Title Utility Functions For GATK. Version 2.1.
Package gsalib February 20, 2015 Type Package Title Utility Functions For GATK Version 2.1 Date 2014-12-09 Author Maintainer Geraldine Van der Auwera This package contains
Package BASiNET. October 2, 2018
Package BASiNET October 2, 2018 Title Classification of RNA Sequences using Complex Network Theory Version 0.0.4 Author Maintainer It makes the creation of networks from sequences
Package reval. May 26, 2015
Package reval May 26, 2015 Title Repeated Function Evaluation for Sensitivity Analysis Version 2.0.0 Date 2015-05-25 Author Michael C Koohafkan [aut, cre] Maintainer Michael C Koohafkan
Package polyphemus. February 15, 2013
Package polyphemus February 15, 2013 Type Package Title Genome wide analysis of RNA Polymerase II-based ChIP Seq data. Version 0.3.4 Date 2010-08-11 Author Martial Sankar, supervised by Marco Mendoza and
Package rgho. R topics documented: January 18, 2017
Package rgho January 18, 2017 Title Access WHO Global Health Observatory Data from R Version 1.0.1 Author Antoine Filipovic-Pierucci [aut,cre] Maintainer Antoine Filipovic-Pierucci
Package jdx. R topics documented: January 9, Type Package Title 'Java' Data Exchange for 'R' and 'rjava'
Type Package Title 'Java' Data Exchange for 'R' and 'rjava' Package jdx January 9, 2018 Description Simplifies and extends data exchange between 'R' and 'Java'. Version 0.1.0 License GPL (>= 2 BSD_3_clause
Package LncPath. May 16, 2016
Type Package Package LncPath May 16, 2016 Title Identifying the Pathways Regulated by LncRNA Sets of Interest Version 1.0 Date 2016-04-27 Author Junwei Han, Zeguo Sun Maintainer Junwei Han
Package ggimage. R topics documented: November 1, Title Use Image in 'ggplot2' Version 0.0.7
Title Use Image in 'ggplot2' Version 0.0.7 Package ggimage November 1, 2017 Supports image files and graphic objects to be visualized in 'ggplot2' graphic system. Depends R (>= 3.3.0), ggplot2 Imports
Package rgreat. June 19, 2018
Type Package Title Client for GREAT Analysis Version 1.12.0 Date 2018-2-20 Author Zuguang Gu Maintainer Zuguang Gu Package rgreat June 19, 2018 Depends R (>= 3.1.2), GenomicRanges, IRanges,
Package wrswor. R topics documented: February 2, Type Package
Type Package Package wrswor February 2, 2018 Title Weighted Random Sampling without Replacement Version 1.1 Date 2018-02-02 Description A collection of implementations of classical and novel algorithms
Package gtrendsr. August 4, 2018
Type Package Title Perform and Display Google Trends Queries Version 1.4.2 Date 2018-08-03 Package gtrendsr August 4, 2018 An interface for retrieving and displaying the information returned online by
Package widyr. August 14, 2017
Type Package Title Widen, Process, then Re-Tidy Data Version 0.1.0 Package widyr August 14, 2017 Encapsulates the pattern of untidying data into a wide matrix, performing some processing, then turning
Package phrasemachine
Type Package Title Simple Phrase Extraction Version 1.1.2 Date 2017-05-29 Package phrasemachine May 29, 2017 Author Matthew J. Denny, Abram Handler, Brendan O'Connor Maintainer Matthew J. Denny
Package catenary. May 4, 2018
Type Package Title Fits a Catenary to Given Points Version 1.1.2 Date 2018-05-04 Package catenary May 4, 2018 Gives methods to create a catenary object and then plot it and get properties of it. Can construct
Package epitab. July 4, 2018
Type Package Package epitab July 4, 2018 Title Flexible Contingency Tables for Epidemiology Version 0.2.2 Author Stuart Lacy Maintainer Stuart Lacy Builds contingency tables that
Package LOLA. December 24, 2018
Package LOLA December 24, 2018 Version 1.13.0 Date 2015-06-26 Title Locus overlap analysis for enrichment of genomic ranges Provides functions for testing overlap of sets of genomic regions with public
Package benchmarkme. R topics documented: February 26, Type Package Title Crowd Sourced System Benchmarks Version 0.2.
Type Package Title Crowd Sourced System Benchmarks Version 0.2.3 Date 2016-02-26 Package benchmarkme February 26, 2016 Maintainer Colin Gillespie Benchmark your CPU and compare
Package svalues. July 15, 2018
Type Package Package svalues July 15, 2018 Title Measures of the Sturdiness of Regression Coefficients Version 0.1.6 Author Carlos Cinelli Maintainer Carlos Cinelli Implements
Package methylgsa. March 7, 2019
Package methylgsa March 7, 2019 Type Package Title Gene Set Analysis Using the Outcome of Differential Methylation Version 1.1.3 The main functions for methylgsa are methylglm and methylrra. methylgsa
Package fastqcr. April 11, 2017
Type Package Title Quality Control of Sequencing Data Version 0.1.0 Date 2017-04-12 Package fastqcr April 11, 2017 'FASTQC' is the most widely used tool for evaluating the quality of high throughput sequencing
Package conumee. February 17, 2018
Package conumee February 17, 2018 Title Enhanced copy-number variation analysis using Illumina DNA methylation arrays Version 1.13.0 Author Volker Hovestadt, Marc Zapatka Maintainer Address Division of
Package condusco. November 8, 2017
Type Package Package condusco November 8, 2017 Title Query-Driven Pipeline Execution and Query Templates Version 0.1.0 Author Roland Stevenson Maintainer Roland Stevenson Description
Package RAPIDR. R topics documented: February 19, 2015
Package RAPIDR February 19, 2015 Title Reliable Accurate Prenatal non-invasive Diagnosis R package Package to perform non-invasive fetal testing for aneuploidies using sequencing count data from cell-free
Package docxtools. July 6, 2018
Title Tools for R Markdown to Docx Documents Version 0.2.0 Language en-us Package docxtools July 6, 2018 A set of helper functions for using R Markdown to create documents in docx format, especially documents
Package splithalf. March 17, 2018
Type Package Package splithalf March 17, 2018 Title Calculate Task Split Half Reliability Estimates Version 0.3.1 Maintainer Sam Parsons A series of functions to calculate the
Practical 4: ChIP-seq Peak calling
Practical 4: ChIP-seq Peak calling Shamith Samarajiiwa, Dora Bihary September 2017 Contents 1 Calling ChIP-seq peaks using MACS2 1 1.1 Assess the quality of the aligned datasets..................................
Package MACPET. January 16, 2019
Type Package Title Model based analysis for paired-end data Version 1.3.0 Date 2018-05-01 Author Ioannis Vardaxis Package MACPET January 16, 2019 Maintainer Ioannis Vardaxis
Package RNAseqNet. May 16, 2017
Type Package Package RNAseqNet May 16, 2017 Title Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation Version 0.1.1 Date 2017-05-16 Maintainer Nathalie Villa-Vialaneix
Package modmarg. R topics documented:
Package modmarg February 1, 2018 Title Calculating Marginal Effects and Levels with Errors Version 0.9.2 Calculate predicted levels and marginal effects, using the delta method to calculate standard errors.
Package liftr. R topics documented: May 14, Type Package
Type Package Package liftr May 14, 2018 Title Containerize R Markdown Documents for Continuous Reproducibility Version 0.9 Maintainer Nan Xiao Persistent reproducible reporting by containerization
Package d3heatmap. February 1, 2018
Type Package Package d3heatmap February 1, 2018 Title Interactive Heat Maps Using 'htmlwidgets' and 'D3.js' Version 0.6.1.2 Date 2016-02-23 Maintainer ORPHANED Description Create interactive heat maps
Package edfreader. R topics documented: May 21, 2017
Type Package Title Reading EDF(+) and BDF(+) Files Version 1.1.2 Date 2017-05-13 Maintainer Jan Vis Package edfreader May 21, 2017 Description Reads European Data Format files EDF
Package kerasformula
Package kerasformula August 23, 2018 Type Package Title A High-Level R Interface for Neural Nets Version 1.5.1 Author Pete Mohanty [aut, cre] Maintainer Pete Mohanty Description
Package bnbc. R topics documented: April 1, Version 1.4.0
Version 1.4.0 Package bnbc April 1, 2019 Title Bandwise normalization and batch correction of Hi-C data Tools to normalize (several) Hi-C data from replicates. Depends R (>= 3.4.0), methods, BiocGenerics,
Package facerec. May 14, 2018
Package facerec Type Package Title An Interface for Face Recognition Version 0.1.0 Date 2018-05-14 May 14, 2018 URL https://github.com/methodds/facerec BugReports https://github.com/methodds/facerec/issues
Package labelvector. July 28, 2018
Title Label Attributes for Atomic Vectors Version 0.1.0 Package labelvector July 28, 2018 Labels are a common construct in statistical software providing a human readable description of a variable. While
Package pomdp. January 3, 2019
Package pomdp January 3, 2019 Title Solver for Partially Observable Markov Decision Processes (POMDP) Version 0.9.1 Date 2019-01-02 Provides an interface to pomdp-solve, a solver for Partially Observable