Packages and data needed for Bioconductor chapters and sections

[smcclatchy]

Level	Chap	Activity	Packages	Data
100	2.3	Introduction to Bioconductor	rtracklayer, GenomicRanges, TxDb.Hsapiens.UCSC.hg38.knownGene, SummarizedExperiment, DESeq2	CpGislands.Hsapiens.hg38.UCSC.bed, airway_counts.csv
201	7.2	Preparing data for DESeq2
201	7.3	Importing into R with tximport	tximportData, TxDb.Hsapiens.UCSC.hg38.knownGene, readr, tximport, jsonlite, DESeq2
201	7.4	Exploratory data analysis	airway, DESeq2, ggplot2	data(airway)
201	7.5	Differential expression analysis	DESeq2, apeglm
201	7.6	AnnotationHub	AnnotationHub
201	7.7	Building reports	ReportingTools, Glimma
201	7.8	Integration with ZINB-WaVE	splatter, zinbwave
LUNCH
102	4.5	Setup	GenomicRanges, AnnotationHub, airway
102	4.6	GRanges: Genomic Ranges	BiocStyle, GenomicRanges
102	4.17	Example: exploring BigWig files from AnnotationHub	AnnotationHub, rtracklayer
102	4.18	Worked example: coverage analysis of BAM files	airway, tools, Rsamtools, GenomicAlignments, GenomicFeatures, EnsDb.Hsapiens.v75	airway(bam files)
COFFEE
101	3.4	Introduction to Bioconductor annotation resources	Bioc2018Anno, hugene20sttranscriptcluster.db, TxDb.Hsapiens.UCSC.hg19.knownGene, EnsDb.Hsapiens.v79, Homo.sapiens, Organism.dplyr, BSgenome, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, biomaRt	Bioc2018Anno(eset.Rdata)
103	5.4	GEOquery	GEOquery, SummarizedExperiment, ggplot2	GEOquery("GSE103512")
103	5.5	GenomicDataCommons	GenomicDataCommons	fnames = lapply(ge_manifest$id[1:20],gdcdata)
103	5.6	Querying metadata	GenomicDataCommons	fnames = gdcdata(manifest_df$id[1:2],progress=FALSE)
103	5.7	Sequence Read Archive	seandavi/SRAdbV2
103	5.8	Accessing The Cancer Genome Atlas (TCGA)	TCGAbiolinks, SummarizedExperiment, curatedTCGAData, MultiAssayExperiment	gdcdir <- file.path("Waldron_PublicData", "GDCdata")
103	5.9	recount: Reproducible RNA-seq Analysis Using recount2	recount
103	5.11	Microbiome data	curatedMetagenomicData, HMP16SData
103	5.12	Pharmacogenomics	PharmacoGx	availablePSets(saveDir=file.path(".", "Waldron_PublicData"))

[smcclatchy]

Hi @jethrojohnson @asliuyar @omsai @dmgatti I've listed packages and data needed for each section of the Bioconductor compilation here.

[duanshumeng]

Warning message: package ‘Bioc2018Anno’ is not available (for R version 3.5.3) I have tried to intsall "Bioc2018Anno" in many ways, but I can do it. I hope you can give me some helps. Thank you very much.

[omsai]

@duanshumeng You're right, Bioc2018Anno is not on Bioconductor. It was a package created specifically for the R / Bioconductor conference 2018 and is available on GitHub only: https://github.com/jmacdon/Bioc2018Anno ... If you add slashes (/) before the package name, BiocManager finds the package on GitHub under the user or organization:

BiocManager::install("jmacdon/Bioc2018Anno")

[sagay2022]

I am attempting to complete this workshop, and I am unable to download and install any of these packages. Please advise. @omsai

[omsai]

I am attempting to complete this workshop, and I am unable to download and install any of these packages. Please advise. @omsai

Can you paste the error you're seeing and your R sessionInfo() please? Also the output of BiocManager::valid() would help.

[sagay2022]

sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] rtracklayer_1.52.0 GenomicRanges_1.44.0 GenomeInfoDb_1.28.0 [4] IRanges_2.26.0 S4Vectors_0.30.0 BiocGenerics_0.38.0 [7] BiocManager_1.30.15

loaded via a namespace (and not attached): [1] XVector_0.32.0 zlibbioc_1.38.0
[3] GenomicAlignments_1.28.0 BiocParallel_1.26.0
[5] lattice_0.20-44 rjson_0.2.20
[7] tools_4.1.0 grid_4.1.0
[9] SummarizedExperiment_1.22.0 Biobase_2.52.0
[11] xfun_0.23 tinytex_0.31
[13] matrixStats_0.58.0 yaml_2.2.1
[15] crayon_1.4.1 BiocIO_1.2.0
[17] Matrix_1.3-3 GenomeInfoDbData_1.2.6
[19] restfulr_0.0.13 bitops_1.0-7
[21] RCurl_1.98-1.3 DelayedArray_0.18.0
[23] compiler_4.1.0 MatrixGenerics_1.4.0
[25] Biostrings_2.60.0 Rsamtools_2.8.0
[27] XML_3.99-0.6

BiocManager::valid() 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

• sessionInfo()

R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] rtracklayer_1.52.0 GenomicRanges_1.44.0 GenomeInfoDb_1.28.0 [4] IRanges_2.26.0 S4Vectors_0.30.0 BiocGenerics_0.38.0 [7] BiocManager_1.30.15

loaded via a namespace (and not attached): [1] XVector_0.32.0 zlibbioc_1.38.0
[3] GenomicAlignments_1.28.0 BiocParallel_1.26.0
[5] lattice_0.20-44 rjson_0.2.20
[7] tools_4.1.0 grid_4.1.0
[9] SummarizedExperiment_1.22.0 Biobase_2.52.0
[11] xfun_0.23 tinytex_0.31
[13] matrixStats_0.58.0 yaml_2.2.1
[15] crayon_1.4.1 BiocIO_1.2.0
[17] Matrix_1.3-3 GenomeInfoDbData_1.2.6
[19] restfulr_0.0.13 bitops_1.0-7
[21] RCurl_1.98-1.3 DelayedArray_0.18.0
[23] compiler_4.1.0 MatrixGenerics_1.4.0
[25] Biostrings_2.60.0 Rsamtools_2.8.0
[27] XML_3.99-0.6

Bioconductor version '3.13'

• 1 packages out-of-date
• 0 packages too new

create a valid installation with

BiocManager::install("stringi", update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message: 1 packages out-of-date; 0 packages too new

[omsai]

@sagay2022 Sorry for the delay: I needed to upgrade to R 4.1.0 and run a few tests. Run these commands to install the required packages for the lessons mentioned in Sue's top comment:

options(timeout = 1000)  # Increase from default 60 sec to download large Bioconductor packages.
options(Ncpus = parallel::detectCores())  # Speed up installation by using all CPU cores.
BiocManager::install("remotes")  # To install packages from GitHub like  "Bioc2018Anno"
BiocManager::install(c("rtracklayer", "TxDb.Hsapiens.UCSC.hg38.knownGene", "DESeq2", "tximportData", "readr", "jsonlite", "airway", "ggplot2", "apeglm", "AnnotationHub", "ReportingTools", "Glimma", "splatter", "zinbwave", "BiocStyle", "EnsDb.Hsapiens.v75", "jmacdon/Bioc2018Anno", "GEOquery", "GenomicDataCommons", "seandavi/SRAdbV2", "TCGAbiolinks", "curatedTCGAData", "MultiAssayExperiment", "recount", "curatedMetagenomicData", "HMP16SData", "PharmacoGx"))

Let us know how the installation goes.

Edit: I just got back home and can confirm all the packages installed for me.

---

Note to other instructors reading this thread: I tested this by excluding any previous packages by setting the R_LIBS_USER variable to a local directory and also adding that path to via libPaths("$R_LIBS_USER"):

$ export R_LIBS_USER=$PWD/rlib
$ mkdir -vp $R_LIBS_USER
mkdir: created directory '/tmp/rlib'
$ # When you type in each line by hand into R, you will see the bash ">" line continuation characters.
$ # These characters have been removed to make the R command easier to copy and paste.
$ R --vanilla << EOF
local({
.libPaths("$R_LIBS_USER")
options(Ncpus = parallel::detectCores(),
        timeout = 1000)
})
install.packages("BiocManager", repos = "https://cloud.r-project.org")
BiocManager::install("remotes")
BiocManager::install(c("rtracklayer", "TxDb.Hsapiens.UCSC.hg38.knownGene", "DESeq2", "tximportData", "readr", "jsonlite", "airway", "ggplot2", "apeglm", "AnnotationHub", "ReportingTools", "Glimma", "splatter", "zinbwave", "BiocStyle", "EnsDb.Hsapiens.v75", "jmacdon/Bioc2018Anno", "GEOquery", "GenomicDataCommons", "seandavi/SRAdbV2", "TCGAbiolinks", "curatedTCGAData", "MultiAssayExperiment", "recount", "curatedMetagenomicData", "HMP16SData", "PharmacoGx"))
EOF