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LieberInstitute / SPEAQeasy

SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.
http://lieberinstitute.github.io/SPEAQeasy
MIT License
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"How is geneMap$Length generated?" reveals more docs are needed #66

Closed lcolladotor closed 3 years ago

lcolladotor commented 3 years ago

Hi,

I initially got confused myself looking for how geneMap$Length is generated. I don't see it at https://github.com/LieberInstitute/SPEAQeasy/blob/master/scripts/build_annotation_objects.R yet it's used by https://github.com/LieberInstitute/SPEAQeasy/blob/master/scripts/create_count_objects-human.R#L529. I later realized that it comes from featureCounts, specifically from http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf.

Screen Shot 2021-04-08 at 4 28 34 PM

It might be useful to document at http://research.libd.org/SPEAQeasy/ where the different pieces for the RSE objects come from. So that might look like a subsection of http://research.libd.org/SPEAQeasy/outputs.html#main-outputs where we explain where each of the pieces (that don't overlap with say the quality metrics already explained in that section) of the RSE objects come from. That is, the rowRanges() and colData() variables. These do change by feature type (gene and exon are the most similar). I think that this will help new users, particularly those learning about SummarizedExperiment as well. It'll make it clearer which parts are common to RSE objects and which are parts we compute as part of SPEAQeasy.

Best, Leo

R

Here's some R code where derived from https://github.com/LieberInstitute/SPEAQeasy/blob/master/scripts/build_annotation_objects.R where I was trying to see if Length showed up. These files are similar to https://github.com/LieberInstitute/RNAseq-pipeline/blob/master/Annotation/junction_txdb/feature_to_tx-gencode.R although now I realize that the older scripts have geneMap refer to featureCounts files while the newer scripts have different sources of geneMap (one is from Gencode GTFs another is from featureCounts).

Gencode 37

library("rtracklayer")
gencode_file <- "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/gencode.v37.annotation.gtf.gz"
gencode_gtf <- import(gencode_file, format = "gtf")
geneMap <- data.frame(gencode_gtf)

Gencode 25

library("rtracklayer")
gencode_file <- "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz"
gencode_gtf <- import(gencode_file, format = "gtf")
geneMap <- data.frame(gencode_gtf)

R 3.6.3

Gencode 37

```R > library("rtracklayer") > gencode_file <- "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/gencode.v37.annotation.gtf.gz" > gencode_gtf <- import(gencode_file, format = "gtf") trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/gencode.v37.annotation.gtf.gz' Content type 'unknown' length 45208353 bytes (43.1 MB) ================================================== > geneMap <- data.frame(gencode_gtf) > > gencode_gtf GRanges object with 3078635 ranges and 21 metadata columns: seqnames ranges strand | source type score | [1] chr1 11869-14409 + | HAVANA gene [2] chr1 11869-14409 + | HAVANA transcript [3] chr1 11869-12227 + | HAVANA exon [4] chr1 12613-12721 + | HAVANA exon [5] chr1 13221-14409 + | HAVANA exon ... ... ... ... . ... ... ... [3078631] chrM 15888-15953 + | ENSEMBL transcript [3078632] chrM 15888-15953 + | ENSEMBL exon [3078633] chrM 15956-16023 - | ENSEMBL gene [3078634] chrM 15956-16023 - | ENSEMBL transcript [3078635] chrM 15956-16023 - | ENSEMBL exon phase gene_id gene_type [1] ENSG00000223972.5 transcribed_unprocessed_pseudogene [2] ENSG00000223972.5 transcribed_unprocessed_pseudogene [3] ENSG00000223972.5 transcribed_unprocessed_pseudogene [4] ENSG00000223972.5 transcribed_unprocessed_pseudogene [5] ENSG00000223972.5 transcribed_unprocessed_pseudogene ... ... ... ... [3078631] ENSG00000210195.2 Mt_tRNA [3078632] ENSG00000210195.2 Mt_tRNA [3078633] ENSG00000210196.2 Mt_tRNA [3078634] ENSG00000210196.2 Mt_tRNA [3078635] ENSG00000210196.2 Mt_tRNA gene_name level hgnc_id havana_gene [1] DDX11L1 2 HGNC:37102 OTTHUMG00000000961.2 [2] DDX11L1 2 HGNC:37102 OTTHUMG00000000961.2 [3] DDX11L1 2 HGNC:37102 OTTHUMG00000000961.2 [4] DDX11L1 2 HGNC:37102 OTTHUMG00000000961.2 [5] DDX11L1 2 HGNC:37102 OTTHUMG00000000961.2 ... ... ... ... ... [3078631] MT-TT 3 HGNC:7499 [3078632] MT-TT 3 HGNC:7499 [3078633] MT-TP 3 HGNC:7494 [3078634] MT-TP 3 HGNC:7494 [3078635] MT-TP 3 HGNC:7494 transcript_id transcript_type transcript_name [1] [2] ENST00000456328.2 processed_transcript DDX11L1-202 [3] ENST00000456328.2 processed_transcript DDX11L1-202 [4] ENST00000456328.2 processed_transcript DDX11L1-202 [5] ENST00000456328.2 processed_transcript DDX11L1-202 ... ... ... ... [3078631] ENST00000387460.2 Mt_tRNA MT-TT-201 [3078632] ENST00000387460.2 Mt_tRNA MT-TT-201 [3078633] [3078634] ENST00000387461.2 Mt_tRNA MT-TP-201 [3078635] ENST00000387461.2 Mt_tRNA MT-TP-201 transcript_support_level tag havana_transcript [1] [2] 1 basic OTTHUMT00000362751.1 [3] 1 basic OTTHUMT00000362751.1 [4] 1 basic OTTHUMT00000362751.1 [5] 1 basic OTTHUMT00000362751.1 ... ... ... ... [3078631] NA basic [3078632] NA basic [3078633] [3078634] NA basic [3078635] NA basic exon_number exon_id ont protein_id ccdsid [1] [2] [3] 1 ENSE00002234944.1 [4] 2 ENSE00003582793.1 [5] 3 ENSE00002312635.1 ... ... ... ... ... ... [3078631] [3078632] 1 ENSE00001544475.2 [3078633] [3078634] [3078635] 1 ENSE00001544473.2 ------- seqinfo: 25 sequences from an unspecified genome; no seqlengths > head(geneMap) seqnames start end width strand source type score phase 1 chr1 11869 14409 2541 + HAVANA gene NA NA 2 chr1 11869 14409 2541 + HAVANA transcript NA NA 3 chr1 11869 12227 359 + HAVANA exon NA NA 4 chr1 12613 12721 109 + HAVANA exon NA NA 5 chr1 13221 14409 1189 + HAVANA exon NA NA 6 chr1 12010 13670 1661 + HAVANA transcript NA NA gene_id gene_type gene_name level 1 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 2 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 3 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 4 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 5 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 6 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 hgnc_id havana_gene transcript_id 1 HGNC:37102 OTTHUMG00000000961.2 2 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 3 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 4 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 5 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 6 HGNC:37102 OTTHUMG00000000961.2 ENST00000450305.2 transcript_type transcript_name transcript_support_level 1 2 processed_transcript DDX11L1-202 1 3 processed_transcript DDX11L1-202 1 4 processed_transcript DDX11L1-202 1 5 processed_transcript DDX11L1-202 1 6 transcribed_unprocessed_pseudogene DDX11L1-201 NA tag havana_transcript exon_number exon_id ont 1 2 basic OTTHUMT00000362751.1 3 basic OTTHUMT00000362751.1 1 ENSE00002234944.1 4 basic OTTHUMT00000362751.1 2 ENSE00003582793.1 5 basic OTTHUMT00000362751.1 3 ENSE00002312635.1 6 basic OTTHUMT00000002844.2 PGO:0000019 protein_id ccdsid 1 2 3 4 5 6 > sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.16 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] rtracklayer_1.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 [4] IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0 [7] testthat_2.3.2 devtools_2.3.0 usethis_1.6.0 loaded via a namespace (and not attached): [1] compiler_3.6.3 XVector_0.26.0 [3] prettyunits_1.1.1 bitops_1.0-6 [5] remotes_2.1.1 tools_3.6.3 [7] zlibbioc_1.32.0 digest_0.6.25 [9] pkgbuild_1.0.7 pkgload_1.0.2 [11] colorout_1.2-1 lattice_0.20-41 [13] memoise_1.1.0 rlang_0.4.5 [15] Matrix_1.2-18 DelayedArray_0.12.3 [17] cli_2.0.2 GenomeInfoDbData_1.2.2 [19] withr_2.2.0 Biostrings_2.54.0 [21] desc_1.2.0 fs_1.4.1 [23] grid_3.6.3 rprojroot_1.3-2 [25] Biobase_2.46.0 glue_1.4.0 [27] R6_2.4.1 processx_3.4.2 [29] fansi_0.4.1 BiocParallel_1.20.1 [31] XML_3.99-0.3 sessioninfo_1.1.1 [33] callr_3.4.3 magrittr_1.5 [35] matrixStats_0.56.0 GenomicAlignments_1.22.1 [37] Rsamtools_2.2.3 backports_1.1.6 [39] ps_1.3.2 ellipsis_0.3.0 [41] SummarizedExperiment_1.16.1 assertthat_0.2.1 [43] RCurl_1.98-1.2 crayon_1.3.4 ```

Gencode 25

```R > library("rtracklayer") > gencode_file <- "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz" > gencode_gtf <- import(gencode_file, format = "gtf") trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz' Content type 'unknown' length 38817086 bytes (37.0 MB) ================================================== > geneMap <- data.frame(gencode_gtf) > > head(geneMap) seqnames start end width strand source type score phase 1 chr1 11869 14409 2541 + HAVANA gene NA NA 2 chr1 11869 14409 2541 + HAVANA transcript NA NA 3 chr1 11869 12227 359 + HAVANA exon NA NA 4 chr1 12613 12721 109 + HAVANA exon NA NA 5 chr1 13221 14409 1189 + HAVANA exon NA NA 6 chr1 12010 13670 1661 + HAVANA transcript NA NA gene_id gene_type gene_status gene_name 1 ENSG00000223972.5 transcribed_unprocessed_pseudogene KNOWN DDX11L1 2 ENSG00000223972.5 transcribed_unprocessed_pseudogene KNOWN DDX11L1 3 ENSG00000223972.5 transcribed_unprocessed_pseudogene KNOWN DDX11L1 4 ENSG00000223972.5 transcribed_unprocessed_pseudogene KNOWN DDX11L1 5 ENSG00000223972.5 transcribed_unprocessed_pseudogene KNOWN DDX11L1 6 ENSG00000223972.5 transcribed_unprocessed_pseudogene KNOWN DDX11L1 level havana_gene transcript_id 1 2 OTTHUMG00000000961.2 2 2 OTTHUMG00000000961.2 ENST00000456328.2 3 2 OTTHUMG00000000961.2 ENST00000456328.2 4 2 OTTHUMG00000000961.2 ENST00000456328.2 5 2 OTTHUMG00000000961.2 ENST00000456328.2 6 2 OTTHUMG00000000961.2 ENST00000450305.2 transcript_type transcript_status transcript_name 1 2 processed_transcript KNOWN DDX11L1-002 3 processed_transcript KNOWN DDX11L1-002 4 processed_transcript KNOWN DDX11L1-002 5 processed_transcript KNOWN DDX11L1-002 6 transcribed_unprocessed_pseudogene KNOWN DDX11L1-001 transcript_support_level tag havana_transcript exon_number 1 2 1 basic OTTHUMT00000362751.1 3 1 basic OTTHUMT00000362751.1 1 4 1 basic OTTHUMT00000362751.1 2 5 1 basic OTTHUMT00000362751.1 3 6 NA basic OTTHUMT00000002844.2 exon_id ont protein_id ccdsid 1 2 3 ENSE00002234944.1 4 ENSE00003582793.1 5 ENSE00002312635.1 6 PGO:0000019 > sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.16 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] rtracklayer_1.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 [4] IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0 [7] testthat_2.3.2 devtools_2.3.0 usethis_1.6.0 loaded via a namespace (and not attached): [1] compiler_3.6.3 XVector_0.26.0 [3] prettyunits_1.1.1 bitops_1.0-6 [5] remotes_2.1.1 tools_3.6.3 [7] zlibbioc_1.32.0 digest_0.6.25 [9] pkgbuild_1.0.7 pkgload_1.0.2 [11] colorout_1.2-1 lattice_0.20-41 [13] memoise_1.1.0 rlang_0.4.5 [15] Matrix_1.2-18 DelayedArray_0.12.3 [17] cli_2.0.2 GenomeInfoDbData_1.2.2 [19] withr_2.2.0 Biostrings_2.54.0 [21] desc_1.2.0 fs_1.4.1 [23] grid_3.6.3 rprojroot_1.3-2 [25] Biobase_2.46.0 glue_1.4.0 [27] R6_2.4.1 processx_3.4.2 [29] fansi_0.4.1 BiocParallel_1.20.1 [31] XML_3.99-0.3 sessioninfo_1.1.1 [33] callr_3.4.3 magrittr_1.5 [35] matrixStats_0.56.0 GenomicAlignments_1.22.1 [37] Rsamtools_2.2.3 backports_1.1.6 [39] ps_1.3.2 ellipsis_0.3.0 [41] SummarizedExperiment_1.16.1 assertthat_0.2.1 [43] RCurl_1.98-1.2 crayon_1.3.4 ```

R 4.1 (R-devel)

This was the first thing I tried actually.

```R > library("rtracklayer") Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: expand.grid, I, unname Loading required package: IRanges Loading required package: GenomeInfoDb gencode_gtf <- "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/gencode.v37.annotation.gtf.gz" > gencode_gtf <- "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/gencode.v37.annotation.gtf.gz" > gencode_file <- "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/gencode.v37.annotation.gtf.gz" > gencode_gtf <- import(gencode_file, format = "gtf") trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/gencode.v37.annotation.gtf.gz' Content type 'unknown' length 45208353 bytes (43.1 MB) ================================================== geneMap = data.frame(gencode_gtf) > geneMap = data.frame(gencode_gtf) > > gencode_gtf GRanges object with 3078635 ranges and 21 metadata columns: seqnames ranges strand | source type score | [1] chr1 11869-14409 + | HAVANA gene NA [2] chr1 11869-14409 + | HAVANA transcript NA [3] chr1 11869-12227 + | HAVANA exon NA [4] chr1 12613-12721 + | HAVANA exon NA [5] chr1 13221-14409 + | HAVANA exon NA ... ... ... ... . ... ... ... [3078631] chrM 15888-15953 + | ENSEMBL transcript NA [3078632] chrM 15888-15953 + | ENSEMBL exon NA [3078633] chrM 15956-16023 - | ENSEMBL gene NA [3078634] chrM 15956-16023 - | ENSEMBL transcript NA [3078635] chrM 15956-16023 - | ENSEMBL exon NA phase gene_id gene_type gene_name [1] ENSG00000223972.5 transcribed_unproces.. DDX11L1 [2] ENSG00000223972.5 transcribed_unproces.. DDX11L1 [3] ENSG00000223972.5 transcribed_unproces.. DDX11L1 [4] ENSG00000223972.5 transcribed_unproces.. DDX11L1 [5] ENSG00000223972.5 transcribed_unproces.. DDX11L1 ... ... ... ... ... [3078631] ENSG00000210195.2 Mt_tRNA MT-TT [3078632] ENSG00000210195.2 Mt_tRNA MT-TT [3078633] ENSG00000210196.2 Mt_tRNA MT-TP [3078634] ENSG00000210196.2 Mt_tRNA MT-TP [3078635] ENSG00000210196.2 Mt_tRNA MT-TP level hgnc_id havana_gene transcript_id [1] 2 HGNC:37102 OTTHUMG00000000961.2 [2] 2 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 [3] 2 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 [4] 2 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 [5] 2 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 ... ... ... ... ... [3078631] 3 HGNC:7499 ENST00000387460.2 [3078632] 3 HGNC:7499 ENST00000387460.2 [3078633] 3 HGNC:7494 [3078634] 3 HGNC:7494 ENST00000387461.2 [3078635] 3 HGNC:7494 ENST00000387461.2 transcript_type transcript_name transcript_support_level [1] [2] processed_transcript DDX11L1-202 1 [3] processed_transcript DDX11L1-202 1 [4] processed_transcript DDX11L1-202 1 [5] processed_transcript DDX11L1-202 1 ... ... ... ... [3078631] Mt_tRNA MT-TT-201 NA [3078632] Mt_tRNA MT-TT-201 NA [3078633] [3078634] Mt_tRNA MT-TP-201 NA [3078635] Mt_tRNA MT-TP-201 NA tag havana_transcript exon_number exon_id [1] [2] basic OTTHUMT00000362751.1 [3] basic OTTHUMT00000362751.1 1 ENSE00002234944.1 [4] basic OTTHUMT00000362751.1 2 ENSE00003582793.1 [5] basic OTTHUMT00000362751.1 3 ENSE00002312635.1 ... ... ... ... ... [3078631] basic [3078632] basic 1 ENSE00001544475.2 [3078633] [3078634] basic [3078635] basic 1 ENSE00001544473.2 ont protein_id ccdsid [1] [2] [3] [4] [5] ... ... ... ... [3078631] [3078632] [3078633] [3078634] [3078635] ------- seqinfo: 25 sequences from an unspecified genome; no seqlengths > geneMap <- data.frame(gencode_gtf) > > head(geneMap) seqnames start end width strand source type score phase 1 chr1 11869 14409 2541 + HAVANA gene NA NA 2 chr1 11869 14409 2541 + HAVANA transcript NA NA 3 chr1 11869 12227 359 + HAVANA exon NA NA 4 chr1 12613 12721 109 + HAVANA exon NA NA 5 chr1 13221 14409 1189 + HAVANA exon NA NA 6 chr1 12010 13670 1661 + HAVANA transcript NA NA gene_id gene_type gene_name level 1 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 2 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 3 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 4 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 5 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 6 ENSG00000223972.5 transcribed_unprocessed_pseudogene DDX11L1 2 hgnc_id havana_gene transcript_id 1 HGNC:37102 OTTHUMG00000000961.2 2 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 3 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 4 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 5 HGNC:37102 OTTHUMG00000000961.2 ENST00000456328.2 6 HGNC:37102 OTTHUMG00000000961.2 ENST00000450305.2 transcript_type transcript_name transcript_support_level 1 2 processed_transcript DDX11L1-202 1 3 processed_transcript DDX11L1-202 1 4 processed_transcript DDX11L1-202 1 5 processed_transcript DDX11L1-202 1 6 transcribed_unprocessed_pseudogene DDX11L1-201 NA tag havana_transcript exon_number exon_id ont 1 2 basic OTTHUMT00000362751.1 3 basic OTTHUMT00000362751.1 1 ENSE00002234944.1 4 basic OTTHUMT00000362751.1 2 ENSE00003582793.1 5 basic OTTHUMT00000362751.1 3 ENSE00002312635.1 6 basic OTTHUMT00000002844.2 PGO:0000019 protein_id ccdsid 1 2 3 4 5 6 > > head(width(gencode_gtf)) [1] 2541 2541 359 109 1189 1661 > sessionInfo() R Under development (unstable) (2021-03-29 r80130) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] rtracklayer_1.51.5 GenomicRanges_1.43.3 GenomeInfoDb_1.27.8 [4] IRanges_2.25.6 S4Vectors_0.29.9 BiocGenerics_0.37.1 [7] testthat_3.0.2 devtools_2.3.2 usethis_2.0.1 loaded via a namespace (and not attached): [1] SummarizedExperiment_1.21.1 remotes_2.2.0 [3] purrr_0.3.4 lattice_0.20-41 [5] yaml_2.2.1 XML_3.99-0.6 [7] rlang_0.4.10 pkgbuild_1.2.0 [9] glue_1.4.2 withr_2.4.1 [11] BiocParallel_1.25.5 rsthemes_0.2.1.9000 [13] sessioninfo_1.1.1 matrixStats_0.58.0 [15] prompt_1.0.1 GenomeInfoDbData_1.2.4 [17] lifecycle_1.0.0 zlibbioc_1.37.0 [19] MatrixGenerics_1.3.1 Biostrings_2.59.2 [21] memoise_2.0.0 restfulr_0.0.13 [23] Biobase_2.51.0 callr_3.6.0 [25] fastmap_1.1.0 ps_1.6.0 [27] cachem_1.0.4 DelayedArray_0.17.10 [29] desc_1.3.0 pkgload_1.2.0 [31] XVector_0.31.1 fs_1.5.0 [33] Rsamtools_2.7.1 rjson_0.2.20 [35] processx_3.5.0 grid_4.1.0 [37] BiocIO_1.1.2 rprojroot_2.0.2 [39] cli_2.3.1 tools_4.1.0 [41] bitops_1.0-6 magrittr_2.0.1 [43] RCurl_1.98-1.3 crayon_1.4.1 [45] ellipsis_0.3.1 Matrix_1.3-2 [47] prettyunits_1.1.1 assertthat_0.2.1 [49] rstudioapi_0.13 R6_2.5.0 [51] colorout_1.2-2 GenomicAlignments_1.27.2 [53] compiler_4.1.0 ```