Bioconductor: Difference between revisions

Revision as of 13:21, 12 July 2019

Project

Release News

3.9 release
3.8 release
3.7 release
3.6 release
3.5 release

Mirrors

https://www.bioconductor.org/about/mirrors/

Github mirror

https://support.bioconductor.org/p/68824/ Announcement (Update: it is dead)

Japan

http://bioconductor.jp

Package source

R > create Bioconductor repository

Code search

http://search.bioconductor.jp/

BiocManager from CRAN

The reason for using BiocManager instead of biocLite() is mostly to stop sourcing an R script from URL which isn’t so safe. So biocLite() should not be recommended anymore.

It allows to have multiple versions of Bioconductor installed on the same computer. For example, R 3.5 works with Bioconductor 3.7 and 3.8.

On the other hand, setRepositories(ind=1:4) and install.packages() still lets you install Bioconductor packages.

Hacking Bioconductor

BiocPkgTools

BiocPkgTools: Collection of simple tools for learning about Bioc Packages]
https://www.biorxiv.org/content/10.1101/642132v1

BioCExplorer

Explore Bioconductor packages more nicely

source("https://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")
biocLite("biocViews")
devtools::install_github("seandavi/BiocPkgTools")
devtools::install_github("shians/BioCExplorer")
library(BioCExplorer)
bioc_explore()

BiocViews

Software
- AssayDomain
- BiologicalQuestion
- Infrastructure
- ResearchField
- StatisticalMethod
- Technology
- WorkflowStep
AnnotationData
- ChipManufacturer
- ChipName
- CustomArray
- CustomCDF
- CustomDBSchema
- FunctionalAnnotation
- Organism
- PackageType
- SequenceAnnotation
ExperimentData
- AssayDomainData
- DiseaseModel
- OrganismData
- PackageTypeData
- RepositoryData
- ReproducibleResearch
- SpecimenSource
- TechnologyData
Workflow
- AnnotationWorkflow
- BasicWorkflow
- DifferentialSplicingWorkflow
- EpigeneticsWorkflow
- GeneExpressionWorkflow
- GenomicVariantsWorkflow
- ImmunoOncologyWorkflow
- ProteomicsWorkflow
- ResourceQueryingWorkflow
- SingleCellWorkflow

Annotation packages

http://bioconductor.org/help/course-materials/2012/SeattleFeb2012/Annotation.pdf
https://bioconductor.org/help/course-materials/2017/CSAMA/lectures/1-monday/lecture-04-a-annotation-intro/lecture-04a-annotation-intro.html
Making and Utilizing TxDb Objects
Genomic Annotation Resources Introduction to using gene, pathway, gene ontology, homology annotations and the AnnotationHub. Access GO, KEGG, NCBI, Biomart, UCSC, vendor, and other sources.
- AnnotationHub
- OrgDb
- TxDb
- OrganismDb
- BSgenome
- biomaRt
http://genomicsclass.github.io/book/pages/bioc1_annoCheat.html
ensembldb package

Gene centric

AnnotationDbi: Introduction To Bioconductor Annotation Packages

library(hgu133a.db)
library(AnnotationDbi)
k <- head(keys(hgu133a.db, keytype="PROBEID"))
k
# [1] "1007_s_at" "1053_at"   "117_at"    "121_at"    "1255_g_at" "1294_at"
# then call select
select(hgu133a.db, keys=k, columns=c("SYMBOL","GENENAME"), keytype="PROBEID")

# 'select()' returned 1:many mapping between keys and columns
#     PROBEID  SYMBOL                                     GENENAME
# 1 1007_s_at    DDR1  discoidin domain receptor tyrosine kinase 1
# 2 1007_s_at MIR4640                                microRNA 4640
# 3   1053_at    RFC2               replication factor C subunit 2
# 4    117_at   HSPA6 heat shock protein family A (Hsp70) member 6
# 5    121_at    PAX8                                 paired box 8
# 6 1255_g_at  GUCA1A               guanylate cyclase activator 1A
# 7   1294_at    UBA7  ubiquitin like modifier activating enzyme 7
# 8   1294_at MIR5193                                microRNA 5193

Genomic centric

Web based

Workflow

Using Bioconductor for Sequence Data

Some packages

Biobase, GEOquery and limma

How to create an ExpressionSet object from scratch? Here we use the code from GEO2R to help to do this task.

library(Biobase)
library(GEOquery)
library(limma)

# Load series and platform data from GEO

gset <- getGEO("GSE32474", GSEMatrix =TRUE, AnnotGPL=TRUE)
if (length(gset) > 1) idx <- grep("GPL570", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]
# save(gset, file = "~/Downloads/gse32474_gset.rda")
# load("~/Downloads/gse32474_gset.rda")
table(pData(gset)[, "cell line:ch1"])
pData(gset)

# Create an ExpressionSet object from scratch
# We take a shortcut to obtain the pheno data and feature data matrices 
# from the output of getGEO()
phenoDat <- new("AnnotatedDataFrame",
                 data=pData(gset))
featureDat <- new("AnnotatedDataFrame",
                  data=fData(gset))
exampleSet <- ExpressionSet(assayData=exprs(gset),
                            phenoData=phenoDat,
                            featureData=featureDat,
                            annotation="hgu133plus2")
gset <- exampleSet

# Make proper column names to match toptable 
fvarLabels(gset) <- make.names(fvarLabels(gset))

# group names for all samples
gsms <- paste0("00000000111111111XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX",
               "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX",
               "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX",
               "XXXXXXXXXXXXXXXXXXXXXXXX")
sml <- c()
for (i in 1:nchar(gsms)) { sml[i] <- substr(gsms,i,i) }

# Subset an ExpressionSet by eliminating samples marked as "X"
sel <- which(sml != "X")
sml <- sml[sel]
gset <- gset[ ,sel]

# Decide if it is necessary to do a log2 transformation
ex <- exprs(gset)
qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
LogC <- (qx[5] > 100) ||
  (qx[6]-qx[1] > 50 && qx[2] > 0) ||
  (qx[2] > 0 && qx[2] < 1 && qx[4] > 1 && qx[4] < 2)
if (LogC) { ex[which(ex <= 0)] <- NaN
exprs(gset) <- log2(ex) }

# Set up the data and proceed with analysis
sml <- paste("G", sml, sep="")    # set group names
fl <- as.factor(sml)
gset$description <- fl
design <- model.matrix(~ description + 0, gset)
colnames(design) <- levels(fl)
fit <- lmFit(gset, design)
cont.matrix <- makeContrasts(G1-G0, levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit2 <- eBayes(fit2, 0.01)
tT <- topTable(fit2, adjust="fdr", sort.by="B", number=250)

# Display the result with selected columns
tT <- subset(tT, select=c("ID","adj.P.Val","P.Value","t","B","logFC","Gene.symbol","Gene.title"))
tT[1:2, ]
#                  ID  adj.P.Val      P.Value        t        B    logFC Gene.symbol
# 209108_at 209108_at 0.08400054 4.438757e-06 6.686977 3.786222 3.949088      TSPAN6
# 204975_at 204975_at 0.08400054 6.036355e-06 6.520775 3.550036 2.919995        EMP2
#                             Gene.title
# 209108_at                 tetraspanin 6
# 204975_at epithelial membrane protein 2

Biostrings

Find the location of a particular sequence. ?vmatchPattern
https://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/BiostringsBSgenomeOverview.pdf

library(Biostrings) 
library(BSgenome.Hsapiens.UCSC.hg19) 
vmatchPattern("GCGATCGC", Hsapiens)

plyranges

http://bioconductor.org/packages/devel/bioc/vignettes/plyranges/inst/doc/an-introduction.html

Misc

Package release history

https://support.bioconductor.org/p/69657/

Search the DESCRIPTION file (eg. VariantAnnotation package) in github and the release information can be found there.

@@ Line 18: / Line 18: @@
 === From the director of the project ===
-[https://t.co/rfKF3ABFJp?amp=1 useR 2019]
+[https://t.co/rfKF3ABFJp?amp=1 useR 2019] & [https://youtu.be/YEQ5xFewbdA?t=891 youtube]
 == Mirrors ==