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Hi, I am using DiffBind (development version 3.0.5) to identify differential open chromatin regions in two cell groups (control vs treated) using ATAC-seq data. HiCdat: Hi-C data analysis tool. User guide including a tutorial for data pre-processing: user guide. Binaries (note that the MacOSX binary was built on 10.10.1 and in addition tested on 10.8.5). Heatplot calls heatmap.2 in the R package gplots. NOTE: We have changed heatplot scaling in made4 (v 1.19.1) in Bioconductor v2.5. Heatplot by default dual scales the data to limits of -3,3. To reproduce older version of heatplot, use the parameters dualScale=FALSE, scale='row'.
TCGAbiolinks: An R/Bioconductor package for integrative analysis withTCGA data
The aim of TCGAbiolinks is : i) facilitate the TCGA open-accessdata retrieval, ii) prepare the data using the appropriate pre-processingstrategies, iii) provide the means to carry out different standard analysesand iv) allow the user to download a specific version of the data and thusto easily reproduce earlier research results. In more detail, the packageprovides multiple methods for analysis (e.g., differential expression analysis,identifying differentially methylated regions) and methods for visualization(e.g., survival plots, volcano plots, starburst plots) in order to easilydevelop complete analysis pipelines.
Readme
Installation
Manual
Functions in TCGAbiolinks
| Name | Description | |
| PR_status_BRCA | PR_status_BRCA | |
| TCGAvisualize_meanMethylation | Mean methylation boxplot | |
| TCGAanalyze_DEA_Affy | Differentially expression analysis (DEA) using limma package. | |
| TCGAvisualize_oncoprint | Creating a oncoprint | |
| TCGAquery_clinic | Get the clinical information | |
| TCGAprepare_Affy | Prepare CEL files into an AffyBatch. | |
| tabPackage2 | tabPackage2 | |
| TCGAquery_subtype | Retrieve molecular subtypes for a given tumor | |
| TCGAquery_MatchedCoupledSampleTypes | Retrieve multiple tissue types from the same patients. | |
| TCGAprepare_elmer | Prepare the data for ELEMR package | |
| BRCA_rnaseqv2 | BRCA_rnaseqv2 | |
| TCGAanalyze_SurvivalKM | survival analysis (SA) univariate with Kaplan-Meier (KM) method. | |
| TCGAvisualize_SurvivalCoxNET | Survival analysis with univariate Cox regression package (dnet) | |
| TCGAanalyze_EAcomplete | Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and Pathways | |
| dataREAD_df | TCGA data matrix READ | |
| tabSurvKMcompleteDEGs | tabSurvKMcompleteDEGs | |
| TCGAanalyze_Clustering | Hierarchical cluster analysis | |
| ER_status_BRCA | ER_status_BRCA | |
| HER_status_BRCA | HER_status_BRCA | |
| TCGAdownload | Download the data from TCGA using as reference the output from TCGAquery | |
| TCGAanalyze_Preprocessing | Array Array Intensity correlation (AAIC) and correlation boxplot to define outlier | |
| TCGAanalyze_DMR | Differentially methylated regions Analysis | |
| TCGAvisualize_BarPlot | Barplot of subtypes and clinical info in groups of gene expression clustered. | |
| ggbiplot | Biplot for Principal Components using ggplot2 | |
| geneInfo | geneInfo for normalization | |
| TCGAUpdate | TCGAUpdate | |
| TCGAvisualize_profilePlot | Profile plot | |
| TCGAbiolinks | Download data of samples from TCGA | |
| TCGAanalyze_EA | Enrichment analysis of a gene-set with GO [BP,MF,CC] and pathways. | |
| diffmean | Calculate diffmean methylation between two groups | |
| TCGAanalyze_Filtering | Filtering mRNA transcripts and miRNA selecting a threshold. | |
| tabPackageKey | tabPackageKey | |
| TCGAquery_clinicFilt | Filter samples using clinical data | |
| TCGAquery_SampleTypes | Retrieve multiple tissue types not from the same patients. | |
| clinBRCA | Clinical data TCGA BRCA | |
| TCGAvisualize_Heatmap | Heatmap with more sensible behavior using heatmap.plus | |
| TCGAprepare | Read the data from level 3 the experiments and prepare it for downstream analysis into a SummarizedExperiment object. | |
| dataBRCA | TCGA data matrix BRCA | |
| TCGAquery_maf | Get last maf file for the tumor | |
| gender_BRCA | gender_BRCA | |
| stage_BRCA | stage_BRCA | |
| TCGAvisualize_Tables | Visaulize results in format of latex tables. | |
| TCGAanalyze_DEA | Differentially expression analysis (DEA) using edgeR package. | |
| batch.info | TCGA batch information from Biospecimen Metadata Browser | |
| TCGAquery_Social | Finds the number of downloads of a package on CRAN or BIOC andfind questions in website ('bioconductor.org', 'biostars.org', 'stackoverflow). | |
| TCGAvisualize_EAbarplot | barPlot for a complete Enrichment Analysis | |
| TCGAvisualize_starburst | Create starburst plot | |
| TCGAvisualize_PCA | Principal components analysis (PCA) plot | |
| tabDEGsTFPubmed | TCGA data matrix BRCA DEGs Pubmed | |
| BRCA_RNASeqV2_version | TCGA Table with version, number of samples and size (Mbyte) ofBRCA IlluminaHiSeq_RNASeqV2 Level 3 | |
| GeneSplitRegulon | GeneSplitRegulon | |
| TCGAVisualize_volcano | Creates a volcano plot for DNA methylation or expression | |
| TCGAanalyze_survival | Creates survival analysis | |
| TCGAquery_Version | Shows a summary (version, date, number of samples, size of the data) ofall versions of data for a given tumor and platform. | |
| TCGAquery_samplesfilter | Filtering sample output from TCGAquery | |
| TCGAquery_integrate | Filtering common samples among platforms from TCGAquery for the same tumor | |
| TCGAvisualize_mutation | Visualize mutation | |
| dataDEGsFiltLevel | TCGA data matrix BRCA DEGs | |
| clinical_data_site_cancer | clinical_data_site_cancer | |
| calculate.pvalues | Calculate pvalues | |
| dataREAD | TCGA data SummarizedExperiment READ | |
| GenesCutID | GenesCutID | |
| TCGAanalyze_Normalization | normalization mRNA transcripts and miRNA using EDASeq package. | |
| TCGAquery_Investigate | Find most studied TF in pubmed related to a specific cancer, disease, or tissue | |
| TCGAquery | Searches TCGA open-access data providing also latest version of the files. | |
| TCGAanalyze_LevelTab | Adding information related to DEGs genes from DEA as mean values in two conditions. | |
| tabPackage1 | tabPackage1 | |
| No Results! | ||
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Details
| Type | Package |
| Date | 2015-12-13 |
| License | GPL (>= 3) |
| biocViews | DNAMethylation,DifferentialMethylation,GeneRegulation,GeneExpression,MethylationArray,DifferentialExpression,Pathways,Network,Survival |
| VignetteBuilder | knitr |
| LazyData | true |
| URL | https://github.com/BioinformaticsFMRP/TCGAbiolinks |
| BugReports | https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues |
| RoxygenNote | 5.0.1 |
| imports | affy , Biobase , BiocGenerics , biomaRt , circlize , coin , ComplexHeatmap , ConsensusClusterPlus , cowplot , data , data.table , dnet , doParallel , downloader (>= 0.4) , dplyr , EDASeq (>= 2.0.0) , edgeR (>= 3.0.0) , genefilter , GenomicFeatures , GenomicRanges , GGally , ggplot2 , ggrepel , ggthemes , gplots , graphics , grDevices , gtable , httr , igraph , IRanges , knitr , limma , magrittr , matlab , parallel , plyr , RColorBrewer , RCurl , reshape2 , rjson , rvest (>= 0.3.0) , S4Vectors , scales , sjmisc , sjPlot (>= 2.0) , stats , stringr (>= 1.0.0) , SummarizedExperiment , supraHex , survival , TxDb , TxDb.Hsapiens.UCSC.hg19.knownGene , utils , XML , xml2 , xtable |
| depends | base (>= 3.2) , R (>= 3.2) |
| suggests | BiocStyle , devtools , png , rmarkdown , testthat |
| Contributors | Michele Ceccarelli, Houtan Noushmehr, Isabella Castiglioni, Davide Garolini, Thais Sabedot, Tathiane Malta, Catharina Olsen, Gianluca Bontempi, Stefano Pagnotta, Luciano Garofano, Antonio Colaprico, Tiago Silva, Claudia Cava |
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