Open smcclatchy opened 5 years ago
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")) |
Hi @jethrojohnson @asliuyar @omsai @dmgatti I've listed packages and data needed for each section of the Bioconductor compilation here.
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.
@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")
I am attempting to complete this workshop, and I am unable to download and install any of these packages. Please advise. @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.
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/
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'
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
@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