From 7bb1b53e8102b0cf9020a4a21abb648e436e8aa1 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Tue, 14 May 2024 14:51:16 +0000 Subject: [PATCH] cli-147-316 --- 404.html | 6 +- CODE_OF_CONDUCT.html | 6 +- articles/index.html | 6 +- articles/tximeta.html | 382 +++++++++++++++++---------------- authors.html | 8 +- index.html | 12 +- news/index.html | 10 +- pkgdown.yml | 6 +- reference/addCDS.html | 6 +- reference/addExons.html | 6 +- reference/addIds.html | 12 +- reference/getTximetaBFC.html | 6 +- reference/index.html | 6 +- reference/linkedTxome.html | 6 +- reference/makeDGEList.html | 6 +- reference/retrieveCDNA.html | 6 +- reference/retrieveDb.html | 12 +- reference/splitSE.html | 6 +- reference/summarizeToGene.html | 12 +- reference/tximeta-package.html | 11 +- reference/tximeta.html | 10 +- 21 files changed, 274 insertions(+), 267 deletions(-) diff --git a/404.html b/404.html index 0a9e8c8..2735a45 100644 --- a/404.html +++ b/404.html @@ -6,7 +6,7 @@ Page not found (404) • tximeta - + @@ -32,7 +32,7 @@ tximeta - 1.21.4 + 1.23.1 @@ -91,7 +91,7 @@

Page not found (404)

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 8760211..dc6e732 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -1,5 +1,5 @@ -Our Pledge • tximetaOur Pledge • tximeta @@ -17,7 +17,7 @@ tximeta - 1.21.4 + 1.23.1 @@ -106,7 +106,7 @@

Attribution -

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/articles/index.html b/articles/index.html index 4fe80f8..52e6435 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,5 +1,5 @@ -Articles • tximetaArticles • tximeta @@ -17,7 +17,7 @@ tximeta - 1.21.4 + 1.23.1 @@ -65,7 +65,7 @@

All vignettes

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/articles/tximeta.html b/articles/tximeta.html index 0657ade..dddf21c 100644 --- a/articles/tximeta.html +++ b/articles/tximeta.html @@ -6,7 +6,7 @@ Tximeta: transcript quantification import with automatic metadata • tximeta - + @@ -33,7 +33,7 @@ tximeta - 1.21.4 + 1.23.1 @@ -74,7 +74,7 @@

Tximeta: transcript quantification import with

Michael I. Love, Charlotte Soneson, Peter F. Hickey, Rob Patro

-

02/21/2024

+

05/14/2024

Source: vignettes/tximeta.Rmd @@ -202,7 +202,7 @@

Running tximeta## 1 ## found matching linked transcriptome: ## [ LocalEnsembl - Drosophila melanogaster - release 98 ] -## building TxDb with 'GenomicFeatures' package +## building TxDb with 'txdbmaker' package ## Import genomic features from the file as a GRanges object ... OK ## Prepare the 'metadata' data frame ... OK ## Make the TxDb object ... OK @@ -245,9 +245,9 @@

TxDb, EnsDb, and AnnotationHub(Lawrence -2013) to parse the GTF and build a TxDb. For Ensembl GTF -files, tximeta will first attempt to obtain the correct +txdbmaker package (Lawrence 2013) +to parse the GTF and build a TxDb. For Ensembl GTF files, +tximeta will first attempt to obtain the correct EnsDb object using AnnotationHub. The ensembldb package (Rainer, Gatto, and Weichenberger 2019) contains classes and methods for extracting @@ -279,27 +279,27 @@

Pre-computed digests GENCODE Homo sapiens -23-45 +23-46 GENCODE Mus musculus -M6-M34 +M6-M35 Ensembl Homo sapiens -76-111 +76-112 Ensembl Mus musculus -76-111 +76-112 Ensembl Drosophila melanogaster -79-111 +79-112 RefSeq @@ -408,7 +408,7 @@

Retrieve the transcript database -
## loading existing TxDb created: 2024-02-21 14:31:38
+
## loading existing TxDb created: 2024-05-14 14:50:44
## Loading required package: GenomicFeatures
## Loading required package: AnnotationDbi
 
## List of 3
 ##  $ version   :Classes 'package_version', 'numeric_version'  hidden list of 1
-##   ..$ : int [1:3] 1 21 4
+##   ..$ : int [1:3] 1 23 1
 ##  $ type      : chr "salmon"
-##  $ importTime: POSIXct[1:1], format: "2024-02-21 14:31:29"
+## $ importTime: POSIXct[1:1], format: "2024-05-14 14:50:35" 
 str(metadata(se)[["txdbInfo"]])
##  Named chr [1:13] "TxDb" "GenomicFeatures" ...
@@ -918,7 +918,7 @@ 
Linked transcriptomes                release="98", genome="BDGP6.22",
                 fasta=fastaFTP, gtf=gtfPath,
                 jsonFile=jsonFile)
-
## writing linkedTxome to /tmp/Rtmph0AffD/Dm.BDGP6.22.98.plus_salmon-0.14.1.json
+
## writing linkedTxome to /tmp/RtmpiBYUNW/Dm.BDGP6.22.98.plus_salmon-0.14.1.json
## saving linkedTxome in bfc

After running makeLinkedTxome, the connection between this Salmon index (and its digest) with the sources is saved @@ -943,7 +943,7 @@

Linked transcriptomes## 1 ## found matching linked transcriptome: ## [ LocalEnsembl - Drosophila melanogaster - release 98 ] -## building TxDb with 'GenomicFeatures' package +## building TxDb with 'txdbmaker' package ## Import genomic features from the file as a GRanges object ... OK ## Prepare the 'metadata' data frame ... OK ## Make the TxDb object ... OK @@ -1027,13 +1027,13 @@

Clear linkedTxomes## # A tibble: 7 × 10 ## rid rname create_time access_time rpath rtype fpath last_modified_time etag ## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <chr> -## 1 BFC1 link… 2024-02-21… 2024-02-21… /tmp… rela… 1255… NA NA -## 2 BFC2 Dros… 2024-02-21… 2024-02-21… /tmp… rela… 1255… NA NA -## 3 BFC3 txpR… 2024-02-21… 2024-02-21… /tmp… rela… 1255… NA NA -## 4 BFC4 exon… 2024-02-21… 2024-02-21… /tmp… rela… 1255… NA NA -## 5 BFC5 gene… 2024-02-21… 2024-02-21… /tmp… rela… 1255… NA NA -## 6 BFC6 Dros… 2024-02-21… 2024-02-21… /tmp… rela… 1255… NA NA -## 7 BFC7 txpR… 2024-02-21… 2024-02-21… /tmp… rela… 1255… NA NA +## 1 BFC1 link… 2024-05-14… 2024-05-14… /tmp… rela… 2606… NA NA +## 2 BFC2 Dros… 2024-05-14… 2024-05-14… /tmp… rela… 2606… NA NA +## 3 BFC3 txpR… 2024-05-14… 2024-05-14… /tmp… rela… 2606… NA NA +## 4 BFC4 exon… 2024-05-14… 2024-05-14… /tmp… rela… 2606… NA NA +## 5 BFC5 gene… 2024-05-14… 2024-05-14… /tmp… rela… 2606… NA NA +## 6 BFC6 Dros… 2024-05-14… 2024-05-14… /tmp… rela… 2606… NA NA +## 7 BFC7 txpR… 2024-05-14… 2024-05-14… /tmp… rela… 2606… NA NA ## # ℹ 1 more variable: expires <dbl>
@@ -1076,8 +1076,8 @@

Loading linkedTxome JSON files< 
## 1 
 ## found matching linked transcriptome:
 ## [ LocalEnsembl - Drosophila melanogaster - release 98 ]
-## loading existing TxDb created: 2024-02-21 14:31:53
-## loading existing transcript ranges created: 2024-02-21 14:31:54
+## loading existing TxDb created: 2024-05-14 14:50:59 +## loading existing transcript ranges created: 2024-05-14 14:50:59 
## Warning in checkAssays2Txps(assays, txps): 
 ## 
 ## Warning: the annotation is missing some transcripts that were quantified.
@@ -1108,13 +1108,13 @@ 
Clear linkedTxomes again## # A tibble: 7 × 10
 ##   rid   rname create_time access_time rpath rtype fpath last_modified_time etag 
 ##   <chr> <chr> <chr>       <chr>       <chr> <chr> <chr>              <dbl> <chr>
-## 1 BFC2  Dros… 2024-02-21… 2024-02-21… /tmp… rela… 1255…                 NA NA   
-## 2 BFC3  txpR… 2024-02-21… 2024-02-21… /tmp… rela… 1255…                 NA NA   
-## 3 BFC4  exon… 2024-02-21… 2024-02-21… /tmp… rela… 1255…                 NA NA   
-## 4 BFC5  gene… 2024-02-21… 2024-02-21… /tmp… rela… 1255…                 NA NA   
-## 5 BFC6  Dros… 2024-02-21… 2024-02-21… /tmp… rela… 1255…                 NA NA   
-## 6 BFC7  txpR… 2024-02-21… 2024-02-21… /tmp… rela… 1255…                 NA NA   
-## 7 BFC8  link… 2024-02-21… 2024-02-21… /tmp… rela… 1255…                 NA NA   
+## 1 BFC2  Dros… 2024-05-14… 2024-05-14… /tmp… rela… 2606…                 NA NA   
+## 2 BFC3  txpR… 2024-05-14… 2024-05-14… /tmp… rela… 2606…                 NA NA   
+## 3 BFC4  exon… 2024-05-14… 2024-05-14… /tmp… rela… 2606…                 NA NA   
+## 4 BFC5  gene… 2024-05-14… 2024-05-14… /tmp… rela… 2606…                 NA NA   
+## 5 BFC6  Dros… 2024-05-14… 2024-05-14… /tmp… rela… 2606…                 NA NA   
+## 6 BFC7  txpR… 2024-05-14… 2024-05-14… /tmp… rela… 2606…                 NA NA   
+## 7 BFC8  link… 2024-05-14… 2024-05-14… /tmp… rela… 2606…                 NA NA   
 ## # ℹ 1 more variable: expires <dbl>
@@ -1207,153 +1207,155 @@

Session infosession_info()

## ─ Session info ───────────────────────────────────────────────────────────────
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-##  os       Ubuntu 22.04.3 LTS
+##  version  R version 4.4.0 (2024-04-24)
+##  os       Ubuntu 22.04.4 LTS
 ##  system   x86_64, linux-gnu
 ##  ui       X11
 ##  language en
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       UTC
-##  date     2024-02-21
-##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
+##  date     2024-05-14
+##  pandoc   3.1.13 @ /usr/bin/ (via rmarkdown)
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 ## 
 ##  [1] /__w/_temp/Library
 ##  [2] /usr/local/lib/R/site-library
@@ -1364,7 +1366,7 @@ 
Session info
 
References
 

-

+

 

 Lawrence, Wolfgang AND Pagès, Michael AND Huber. 2013. “Software for Computing and Annotating Genomic
 Ranges.” PLOS Computational Biology 9 (8): 1–10.
@@ -1428,7 +1430,7 @@ 
References
   

-
Site built with pkgdown 2.0.7.

+
Site built with pkgdown 2.0.9.

 

 
       
diff --git a/authors.html b/authors.html
index aeda5b1..e85f44c 100644
--- a/authors.html
+++ b/authors.html
@@ -1,5 +1,5 @@
 
-Authors and Citation • tximetaAuthors and Citation • tximeta
@@ -17,7 +17,7 @@
       
       
         tximeta
-        1.21.4
+        1.23.1
       
     

 
@@ -47,7 +47,7 @@
   

     

       

-        
Authors

+        
Authors and Citation

       

 
       
@@ -107,7 +107,7 @@ 
Citation

 

 
 

-  
Site built with pkgdown 2.0.7.

+  
Site built with pkgdown 2.0.9.

 

 
       

diff --git a/index.html b/index.html
index 71f6860..e0d69ab 100644
--- a/index.html
+++ b/index.html
@@ -6,17 +6,13 @@
 
 
 Transcript Quantification Import with Automatic Metadata • tximeta
-
+
 
 
 
 
 
-
+
 Changelog • tximetaChangelog • tximeta
@@ -17,7 +17,7 @@
       
       
         tximeta
-        1.21.4
+        1.23.1
       
     

 
@@ -50,6 +50,10 @@ 
Changelog 

       Source: NEWS.md

+
+

tximeta 1.23.1

+
  • GENCODE 46 (H.s.), M35 (M.m), and Ensembl 112
    • +

tximeta 1.21.4

diff --git a/pkgdown.yml b/pkgdown.yml index 5c5543e..32f2864 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,9 +1,9 @@ -pandoc: 3.1.1 -pkgdown: 2.0.7 +pandoc: 3.1.13 +pkgdown: 2.0.9 pkgdown_sha: ~ articles: tximeta: tximeta.html -last_built: 2024-02-21T14:30Z +last_built: 2024-05-14T14:49Z urls: reference: https://thelovelab.github.io/tximeta/reference article: https://thelovelab.github.io/tximeta/articles diff --git a/reference/addCDS.html b/reference/addCDS.html index 5b2a599..380403c 100644 --- a/reference/addCDS.html +++ b/reference/addCDS.html @@ -1,5 +1,5 @@ -Add CDS to rowRanges of a transcript-level SummarizedExperiment — addCDS • tximetaAdd CDS to rowRanges of a transcript-level SummarizedExperiment — addCDS • tximeta tximeta - 1.21.4 + 1.23.1 @@ -110,7 +110,7 @@

Value

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/addExons.html b/reference/addExons.html index 147a03a..e3e3905 100644 --- a/reference/addExons.html +++ b/reference/addExons.html @@ -1,5 +1,5 @@ -Add exons to rowRanges of a transcript-level SummarizedExperiment — addExons • tximetaAdd exons to rowRanges of a transcript-level SummarizedExperiment — addExons • tximeta tximeta - 1.21.4 + 1.23.1 @@ -113,7 +113,7 @@

Details

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/addIds.html b/reference/addIds.html index a9e25bc..b9ac69e 100644 --- a/reference/addIds.html +++ b/reference/addIds.html @@ -1,5 +1,5 @@ -Add IDs to rowRanges of a SummarizedExperiment — addIds • tximeta tximeta - 1.21.4 + 1.23.1 @@ -140,7 +140,7 @@

Examples

#> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> building TxDb with 'GenomicFeatures' package +#> building TxDb with 'txdbmaker' package #> Import genomic features from the file as a GRanges object ... #> OK #> Prepare the 'metadata' data frame ... @@ -182,8 +182,8 @@

Examples

#> as.data.frame, basename, cbind, colnames, dirname, do.call, #> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, #> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, -#> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, -#> tapply, union, unique, unsplit, which.max, which.min +#> pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, +#> union, unique, unsplit, which.max, which.min #> Loading required package: Biobase #> Welcome to Bioconductor #> @@ -221,7 +221,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/getTximetaBFC.html b/reference/getTximetaBFC.html index 93b7e25..174e455 100644 --- a/reference/getTximetaBFC.html +++ b/reference/getTximetaBFC.html @@ -1,5 +1,5 @@ -Get or set the directory of the BiocFileCache used by tximeta — getTximetaBFC • tximetaGet or set the directory of the BiocFileCache used by tximeta — getTximetaBFC • tximeta tximeta - 1.21.4 + 1.23.1 @@ -117,7 +117,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/index.html b/reference/index.html index 1b66f68..8f8fe74 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,5 +1,5 @@ -Function reference • tximetaFunction reference • tximeta @@ -17,7 +17,7 @@ tximeta - 1.21.4 + 1.23.1 @@ -134,7 +134,7 @@

Other helpers
-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/linkedTxome.html b/reference/linkedTxome.html index e9c5bfc..8f68732 100644 --- a/reference/linkedTxome.html +++ b/reference/linkedTxome.html @@ -1,5 +1,5 @@ -Make and load linked transcriptomes ("linkedTxome") — linkedTxome • tximetaMake and load linked transcriptomes ("linkedTxome") — linkedTxome • tximeta tximeta - 1.21.4 + 1.23.1 @@ -220,7 +220,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/makeDGEList.html b/reference/makeDGEList.html index d332ddf..fb09626 100644 --- a/reference/makeDGEList.html +++ b/reference/makeDGEList.html @@ -1,5 +1,5 @@ -Make a DGEList from tximeta output — makeDGEList • tximetaMake a DGEList from tximeta output — makeDGEList • tximetaRetrieve the cDNA transcript sequence for a SummarizedExperiment — retrieveCDNA • tximetaRetrieve the cDNA transcript sequence for a SummarizedExperiment — retrieveCDNA • tximeta tximeta - 1.21.4 + 1.23.1 @@ -109,7 +109,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/retrieveDb.html b/reference/retrieveDb.html index f493181..71230b8 100644 --- a/reference/retrieveDb.html +++ b/reference/retrieveDb.html @@ -1,5 +1,5 @@ -Retrieve the TxDb or EnsDb associated with a SummarizedExperiment — retrieveDb • tximetaRetrieve the TxDb or EnsDb associated with a SummarizedExperiment — retrieveDb • tximeta tximeta - 1.21.4 + 1.23.1 @@ -115,11 +115,11 @@

Examples

#> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> loading existing TxDb created: 2024-02-21 14:31:11 +#> loading existing TxDb created: 2024-05-14 14:50:17 #> Loading required package: GenomicFeatures #> Loading required package: GenomeInfoDb #> Loading required package: GenomicRanges -#> loading existing transcript ranges created: 2024-02-21 14:31:12 +#> loading existing transcript ranges created: 2024-05-14 14:50:18 #> Warning: #> #> Warning: the annotation is missing some transcripts that were quantified. @@ -140,7 +140,7 @@

Examples

#> tximet> #> tximet> edb <- retrieveDb(se) -#> loading existing TxDb created: 2024-02-21 14:31:11 +#> loading existing TxDb created: 2024-05-14 14:50:17 @@ -156,7 +156,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/splitSE.html b/reference/splitSE.html index 296e58b..560ae2d 100644 --- a/reference/splitSE.html +++ b/reference/splitSE.html @@ -1,5 +1,5 @@ -Split SummarizedExperiment by gene categories — splitSE • tximetaSplit SummarizedExperiment by gene categories — splitSE • tximeta tximeta - 1.21.4 + 1.23.1 @@ -137,7 +137,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/summarizeToGene.html b/reference/summarizeToGene.html index 2cf2e12..22b3d84 100644 --- a/reference/summarizeToGene.html +++ b/reference/summarizeToGene.html @@ -1,5 +1,5 @@ -Summarize estimated quantitites to gene-level — summarizeToGene,SummarizedExperiment-method • tximetaSummarize estimated quantitites to gene-level — summarizeToGene,SummarizedExperiment-method • tximeta tximeta - 1.21.4 + 1.23.1 @@ -156,8 +156,8 @@

Examples

#> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> loading existing TxDb created: 2024-02-21 14:31:11 -#> loading existing transcript ranges created: 2024-02-21 14:31:12 +#> loading existing TxDb created: 2024-05-14 14:50:17 +#> loading existing transcript ranges created: 2024-05-14 14:50:18 #> Warning: #> #> Warning: the annotation is missing some transcripts that were quantified. @@ -178,7 +178,7 @@

Examples

#> tximet> #> tximet> gse <- summarizeToGene(se) -#> loading existing TxDb created: 2024-02-21 14:31:11 +#> loading existing TxDb created: 2024-05-14 14:50:17 #> obtaining transcript-to-gene mapping from database #> generating gene ranges #> gene ranges assigned by total range of isoforms, see `assignRanges` @@ -200,7 +200,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/tximeta-package.html b/reference/tximeta-package.html index 02cd853..e2d4667 100644 --- a/reference/tximeta-package.html +++ b/reference/tximeta-package.html @@ -1,5 +1,5 @@ -Import transcript quantification with metadata — tximeta-package • tximetaImport transcript quantification with metadata — tximeta-package • tximeta tximeta - 1.21.4 + 1.23.1 @@ -99,6 +99,11 @@

References

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research. http://doi.org/10.12688/f1000research.7563

+ +
+

See also

+

Useful links:

Author

@@ -117,7 +122,7 @@

Author

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/reference/tximeta.html b/reference/tximeta.html index aa988c4..27d4b02 100644 --- a/reference/tximeta.html +++ b/reference/tximeta.html @@ -1,5 +1,5 @@ -Import transcript quantification with metadata — tximeta • tximetaImport transcript quantification with metadata — tximeta • tximeta tximeta - 1.21.4 + 1.23.1 @@ -222,8 +222,8 @@

Examples

#> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> loading existing TxDb created: 2024-02-21 14:31:11 -#> loading existing transcript ranges created: 2024-02-21 14:31:12 +#> loading existing TxDb created: 2024-05-14 14:50:17 +#> loading existing transcript ranges created: 2024-05-14 14:50:18 #> Warning: #> #> Warning: the annotation is missing some transcripts that were quantified. @@ -254,7 +254,7 @@

Examples

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.