From bf80bea8ecc460c5c8c186876e710f8a37061e75 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Sat, 8 Jun 2024 13:09:44 +0000 Subject: [PATCH] cli-147-316 --- 404.html | 2 +- CODE_OF_CONDUCT.html | 2 +- articles/index.html | 2 +- articles/tximeta.html | 168 +++++++++++++++++---------------- authors.html | 2 +- index.html | 2 +- news/index.html | 2 +- pkgdown.yml | 2 +- reference/addCDS.html | 2 +- reference/addExons.html | 2 +- reference/addIds.html | 2 +- reference/getTximetaBFC.html | 2 +- reference/index.html | 2 +- reference/linkedTxome.html | 2 +- reference/makeDGEList.html | 2 +- reference/retrieveCDNA.html | 2 +- reference/retrieveDb.html | 8 +- reference/splitSE.html | 2 +- reference/summarizeToGene.html | 11 ++- reference/tximeta-package.html | 2 +- reference/tximeta.html | 6 +- 21 files changed, 115 insertions(+), 112 deletions(-) diff --git a/404.html b/404.html index 2735a45..f5750e7 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index dc6e732..7f758d4 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/articles/index.html b/articles/index.html index 52e6435..bdb5f38 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/articles/tximeta.html b/articles/tximeta.html index dddf21c..820a086 100644 --- a/articles/tximeta.html +++ b/articles/tximeta.html @@ -33,7 +33,7 @@ tximeta - 1.23.1 + 1.23.2 @@ -74,7 +74,7 @@

Tximeta: transcript quantification import with

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

-

05/14/2024

+

06/08/2024

Source: vignettes/tximeta.Rmd @@ -408,7 +408,7 @@

Retrieve the transcript database -
## loading existing TxDb created: 2024-05-14 14:50:44
+
## loading existing TxDb created: 2024-06-08 13:09:13
## Loading required package: GenomicFeatures
## Loading required package: AnnotationDbi
@@ -443,7 +443,7 @@ 
Add exons per transcript
 
-
## loading existing TxDb created: 2024-05-14 14:50:44

+
## loading existing TxDb created: 2024-06-08 13:09:13

 
## generating exon ranges

 
 rowRanges(se.exons)[[1]]

@@ -482,10 +482,11 @@ 
Easy summarization to gene-leveltx_ids.

 
 gse <- summarizeToGene(se)

-
## loading existing TxDb created: 2024-05-14 14:50:44

+
## loading existing TxDb created: 2024-06-08 13:09:13

 
## obtaining transcript-to-gene mapping from database

 
## generating gene ranges

-
## gene ranges assigned by total range of isoforms, see `assignRanges`

+
## assignRanges='range': gene ranges assigned by total range of isoforms
+##   see details at: ?summarizeToGene,SummarizedExperiment-method

 
## summarizing abundance

 
## summarizing counts

 
## summarizing length

@@ -639,10 +640,11 @@ 
Differential expression analysis
 
 gse <- summarizeToGene(se, countsFromAbundance="lengthScaledTPM")

-
## loading existing TxDb created: 2024-05-14 14:50:44

+
## loading existing TxDb created: 2024-06-08 13:09:13

 
## obtaining transcript-to-gene mapping from database

-
## loading existing gene ranges created: 2024-05-14 14:50:47

-
## gene ranges assigned by total range of isoforms, see `assignRanges`

+
## loading existing gene ranges created: 2024-06-08 13:09:17

+
## assignRanges='range': gene ranges assigned by total range of isoforms
+##   see details at: ?summarizeToGene,SummarizedExperiment-method

 
## summarizing abundance

 
## summarizing counts

 
## summarizing length

@@ -718,9 +720,9 @@ 
Additional metadatastr(metadata(se)[["tximetaInfo"]])
## List of 3
 ##  $ version   :Classes 'package_version', 'numeric_version'  hidden list of 1
-##   ..$ : int [1:3] 1 23 1
+##   ..$ : int [1:3] 1 23 2
 ##  $ type      : chr "salmon"
-##  $ importTime: POSIXct[1:1], format: "2024-05-14 14:50:35"
+## $ importTime: POSIXct[1:1], format: "2024-06-08 13:09:05" 
 str(metadata(se)[["txdbInfo"]])
##  Named chr [1:13] "TxDb" "GenomicFeatures" ...
@@ -918,7 +920,7 @@ 
Linked transcriptomes                release="98", genome="BDGP6.22",
                 fasta=fastaFTP, gtf=gtfPath,
                 jsonFile=jsonFile)
-
## writing linkedTxome to /tmp/RtmpiBYUNW/Dm.BDGP6.22.98.plus_salmon-0.14.1.json
+
## writing linkedTxome to /tmp/RtmpLZTW6v/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 @@ -1027,13 +1029,13 @@

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… 2024-05-14… 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 +## 1 BFC1 link… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA +## 2 BFC2 Dros… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA +## 3 BFC3 txpR… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA +## 4 BFC4 exon… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA +## 5 BFC5 gene… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA +## 6 BFC6 Dros… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA +## 7 BFC7 txpR… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA ## # ℹ 1 more variable: expires <dbl>
@@ -1076,8 +1078,8 @@

Loading linkedTxome JSON files< 
## 1 
 ## found matching linked transcriptome:
 ## [ LocalEnsembl - Drosophila melanogaster - release 98 ]
-## loading existing TxDb created: 2024-05-14 14:50:59
-## loading existing transcript ranges created: 2024-05-14 14:50:59
+## loading existing TxDb created: 2024-06-08 13:09:29 +## loading existing transcript ranges created: 2024-06-08 13:09:29 
## Warning in checkAssays2Txps(assays, txps): 
 ## 
 ## Warning: the annotation is missing some transcripts that were quantified.
@@ -1108,13 +1110,13 @@ 
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… 2024-05-14… 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   
+## 1 BFC2  Dros… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
+## 2 BFC3  txpR… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
+## 3 BFC4  exon… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
+## 4 BFC5  gene… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
+## 5 BFC6  Dros… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
+## 6 BFC7  txpR… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
+## 7 BFC8  link… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
 ## # ℹ 1 more variable: expires <dbl>
@@ -1215,12 +1217,12 @@

Session info## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz UTC -## date 2024-05-14 +## date 2024-06-08 ## pandoc 3.1.13 @ /usr/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source -## abind 1.4-5 2016-07-21 [1] CRAN (R 4.4.0) +## abind 1.4-5 2016-07-21 [1] RSPM (R 4.4.0) ## AnnotationDbi * 1.66.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.0) ## AnnotationFilter 1.28.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## AnnotationHub 3.12.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) @@ -1232,47 +1234,47 @@

Session info## BiocParallel 1.38.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## BiocVersion 3.19.1 2024-04-17 [2] Bioconductor 3.19 (R 4.4.0) ## biomaRt 2.60.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) -## Biostrings 2.72.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) -## bit 4.0.5 2022-11-15 [1] CRAN (R 4.4.0) -## bit64 4.0.5 2020-08-30 [1] CRAN (R 4.4.0) -## bitops 1.0-7 2021-04-24 [1] CRAN (R 4.4.0) -## blob 1.2.4 2023-03-17 [1] CRAN (R 4.4.0) +## Biostrings 2.72.1 2024-06-02 [1] Bioconductor 3.19 (R 4.4.0) +## bit 4.0.5 2022-11-15 [1] RSPM (R 4.4.0) +## bit64 4.0.5 2020-08-30 [1] RSPM (R 4.4.0) +## bitops 1.0-7 2021-04-24 [1] RSPM (R 4.4.0) +## blob 1.2.4 2023-03-17 [1] RSPM (R 4.4.0) ## bslib 0.7.0 2024-03-29 [2] RSPM (R 4.4.0) -## cachem 1.0.8 2023-05-01 [2] RSPM (R 4.4.0) +## cachem 1.1.0 2024-05-16 [2] RSPM (R 4.4.0) ## cli 3.6.2 2023-12-11 [2] RSPM (R 4.4.0) ## codetools 0.2-20 2024-03-31 [3] CRAN (R 4.4.0) -## colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.4.0) +## colorspace 2.1-0 2023-01-23 [1] RSPM (R 4.4.0) ## crayon 1.5.2 2022-09-29 [2] RSPM (R 4.4.0) ## curl 5.2.1 2024-03-01 [2] RSPM (R 4.4.0) -## DBI 1.2.2 2024-02-16 [1] RSPM (R 4.4.0) +## DBI 1.2.3 2024-06-02 [1] RSPM (R 4.4.0) ## dbplyr * 2.5.0 2024-03-19 [1] RSPM (R 4.4.0) ## DelayedArray 0.30.1 2024-05-07 [1] Bioconductor 3.19 (R 4.4.0) ## desc 1.4.3 2023-12-10 [2] RSPM (R 4.4.0) ## DESeq2 * 1.44.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## devtools * 2.4.5 2022-10-11 [2] RSPM (R 4.4.0) ## digest 0.6.35 2024-03-11 [2] RSPM (R 4.4.0) -## dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.4.0) +## dplyr 1.1.4 2023-11-17 [1] RSPM (R 4.4.0) ## edgeR * 4.2.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## ellipsis 0.3.2 2021-04-29 [2] RSPM (R 4.4.0) ## ensembldb 2.28.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## evaluate 0.23 2023-11-01 [2] RSPM (R 4.4.0) ## fansi 1.0.6 2023-12-08 [2] RSPM (R 4.4.0) -## fastmap 1.1.1 2023-02-24 [2] RSPM (R 4.4.0) -## filelock 1.0.3 2023-12-11 [1] CRAN (R 4.4.0) +## fastmap 1.2.0 2024-05-15 [2] RSPM (R 4.4.0) +## filelock 1.0.3 2023-12-11 [1] RSPM (R 4.4.0) ## fishpond * 2.10.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## fs 1.6.4 2024-04-25 [2] RSPM (R 4.4.0) -## generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0) -## GenomeInfoDb * 1.40.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) -## GenomeInfoDbData 1.2.12 2024-05-14 [1] Bioconductor +## generics 0.1.3 2022-07-05 [1] RSPM (R 4.4.0) +## GenomeInfoDb * 1.40.1 2024-05-24 [1] Bioconductor 3.19 (R 4.4.0) +## GenomeInfoDbData 1.2.12 2024-05-26 [1] Bioconductor ## GenomicAlignments 1.40.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## GenomicFeatures * 1.56.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## GenomicRanges * 1.56.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.0) ## ggplot2 3.5.1 2024-04-23 [1] RSPM (R 4.4.0) ## glue 1.7.0 2024-01-09 [2] RSPM (R 4.4.0) ## gtable 0.3.5 2024-04-22 [1] RSPM (R 4.4.0) -## gtools 3.9.5 2023-11-20 [1] CRAN (R 4.4.0) -## highr 0.10 2022-12-22 [2] RSPM (R 4.4.0) -## hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0) +## gtools 3.9.5 2023-11-20 [1] RSPM (R 4.4.0) +## highr 0.11 2024-05-26 [2] RSPM (R 4.4.0) +## hms 1.1.3 2023-03-21 [1] RSPM (R 4.4.0) ## htmltools 0.5.8.1 2024-04-04 [2] RSPM (R 4.4.0) ## htmlwidgets 1.6.4 2023-12-06 [2] RSPM (R 4.4.0) ## httpuv 1.6.15 2024-03-26 [2] RSPM (R 4.4.0) @@ -1282,12 +1284,12 @@

Session info## jquerylib 0.1.4 2021-04-26 [2] RSPM (R 4.4.0) ## jsonlite 1.8.8 2023-12-04 [2] RSPM (R 4.4.0) ## KEGGREST 1.44.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) -## knitr 1.46 2024-04-06 [2] RSPM (R 4.4.0) +## knitr 1.47 2024-05-29 [2] RSPM (R 4.4.0) ## later 1.3.2 2023-12-06 [2] RSPM (R 4.4.0) ## lattice 0.22-6 2024-03-20 [3] CRAN (R 4.4.0) -## lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.4.0) +## lazyeval 0.2.2 2019-03-15 [1] RSPM (R 4.4.0) ## lifecycle 1.0.4 2023-11-07 [2] RSPM (R 4.4.0) -## limma * 3.60.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) +## limma * 3.60.2 2024-05-19 [1] Bioconductor 3.19 (R 4.4.0) ## locfit 1.5-9.9 2024-03-01 [1] RSPM (R 4.4.0) ## magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.4.0) ## Matrix 1.7-0 2024-03-22 [3] CRAN (R 4.4.0) @@ -1297,51 +1299,51 @@

Session info## mime 0.12 2021-09-28 [2] RSPM (R 4.4.0) ## miniUI 0.1.1.1 2018-05-18 [2] RSPM (R 4.4.0) ## munsell 0.5.1 2024-04-01 [1] RSPM (R 4.4.0) -## org.Dm.eg.db * 3.19.1 2024-05-14 [1] Bioconductor +## org.Dm.eg.db * 3.19.1 2024-05-27 [1] Bioconductor ## pillar 1.9.0 2023-03-22 [2] RSPM (R 4.4.0) ## pkgbuild 1.4.4 2024-03-17 [2] RSPM (R 4.4.0) ## pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.4.0) ## pkgdown 2.0.9 2024-04-18 [2] RSPM (R 4.4.0) ## pkgload 1.3.4 2024-01-16 [2] RSPM (R 4.4.0) -## png 0.1-8 2022-11-29 [1] CRAN (R 4.4.0) +## png 0.1-8 2022-11-29 [1] RSPM (R 4.4.0) ## prettyunits 1.2.0 2023-09-24 [2] RSPM (R 4.4.0) ## profvis 0.3.8 2023-05-02 [2] RSPM (R 4.4.0) -## progress 1.2.3 2023-12-06 [1] CRAN (R 4.4.0) +## progress 1.2.3 2023-12-06 [1] RSPM (R 4.4.0) ## promises 1.3.0 2024-04-05 [2] RSPM (R 4.4.0) ## ProtGenerics 1.36.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## purrr 1.0.2 2023-08-10 [2] RSPM (R 4.4.0) ## R6 2.5.1 2021-08-19 [2] RSPM (R 4.4.0) -## ragg 1.3.1 2024-05-06 [2] RSPM (R 4.4.0) +## ragg 1.3.2 2024-05-15 [2] RSPM (R 4.4.0) ## rappdirs 0.3.3 2021-01-31 [2] RSPM (R 4.4.0) ## Rcpp 1.0.12 2024-01-09 [2] RSPM (R 4.4.0) -## RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.4.0) -## remotes 2.5.0.9000 2024-05-14 [1] Github (r-lib/remotes@5b7eb08) -## restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.4.0) -## rjson 0.2.21 2022-01-09 [1] CRAN (R 4.4.0) -## rlang 1.1.3 2024-01-10 [2] RSPM (R 4.4.0) -## rmarkdown 2.26 2024-03-05 [2] RSPM (R 4.4.0) +## RCurl 1.98-1.14 2024-01-09 [1] RSPM (R 4.4.0) +## remotes 2.5.0.9000 2024-06-08 [1] Github (r-lib/remotes@5b7eb08) +## restfulr 0.0.15 2022-06-16 [1] RSPM (R 4.4.0) +## rjson 0.2.21 2022-01-09 [1] RSPM (R 4.4.0) +## rlang 1.1.4 2024-06-04 [2] RSPM (R 4.4.0) +## rmarkdown 2.27 2024-05-17 [2] RSPM (R 4.4.0) ## Rsamtools 2.20.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) -## RSQLite 2.3.6 2024-03-31 [1] RSPM (R 4.4.0) +## RSQLite 2.3.7 2024-05-27 [1] RSPM (R 4.4.0) ## rtracklayer 1.64.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) -## S4Arrays 1.4.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) +## S4Arrays 1.4.1 2024-05-20 [1] Bioconductor 3.19 (R 4.4.0) ## S4Vectors * 0.42.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## sass 0.4.9 2024-03-15 [2] RSPM (R 4.4.0) -## scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0) +## scales 1.3.0 2023-11-28 [1] RSPM (R 4.4.0) ## sessioninfo 1.2.2 2021-12-06 [2] RSPM (R 4.4.0) ## shiny 1.8.1.1 2024-04-02 [2] RSPM (R 4.4.0) ## SingleCellExperiment 1.26.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) -## SparseArray 1.4.3 2024-05-07 [1] Bioconductor 3.19 (R 4.4.0) -## statmod 1.5.0 2023-01-06 [1] CRAN (R 4.4.0) +## SparseArray 1.4.8 2024-05-24 [1] Bioconductor 3.19 (R 4.4.0) +## statmod 1.5.0 2023-01-06 [1] RSPM (R 4.4.0) ## stringi 1.8.4 2024-05-06 [2] RSPM (R 4.4.0) ## stringr 1.5.1 2023-11-14 [2] RSPM (R 4.4.0) ## SummarizedExperiment * 1.34.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.0) -## svMisc 1.2.3 2021-10-11 [1] CRAN (R 4.4.0) -## systemfonts 1.0.6 2024-03-07 [2] RSPM (R 4.4.0) -## textshaping 0.3.7 2023-10-09 [2] RSPM (R 4.4.0) +## svMisc 1.2.3 2021-10-11 [1] RSPM (R 4.4.0) +## systemfonts 1.1.0 2024-05-15 [2] RSPM (R 4.4.0) +## textshaping 0.4.0 2024-05-24 [2] RSPM (R 4.4.0) ## tibble 3.2.1 2023-03-20 [2] RSPM (R 4.4.0) ## tidyselect 1.2.1 2024-03-11 [1] RSPM (R 4.4.0) ## txdbmaker 1.0.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) -## tximeta * 1.23.1 2024-05-14 [1] Bioconductor +## tximeta * 1.23.2 2024-06-08 [1] Bioconductor ## tximport 1.32.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## UCSC.utils 1.0.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) ## urlchecker 1.0.1 2021-11-30 [2] RSPM (R 4.4.0) @@ -1349,8 +1351,8 @@

Session info## utf8 1.2.4 2023-10-22 [2] RSPM (R 4.4.0) ## vctrs 0.6.5 2023-12-01 [2] RSPM (R 4.4.0) ## withr 3.0.0 2024-01-16 [2] RSPM (R 4.4.0) -## xfun 0.43 2024-03-25 [2] RSPM (R 4.4.0) -## XML 3.99-0.16.1 2024-01-22 [1] CRAN (R 4.4.0) +## xfun 0.44 2024-05-15 [2] RSPM (R 4.4.0) +## XML 3.99-0.16.1 2024-01-22 [1] RSPM (R 4.4.0) ## xml2 1.3.6 2023-12-04 [2] RSPM (R 4.4.0) ## xtable 1.8-4 2019-04-21 [2] RSPM (R 4.4.0) ## XVector 0.44.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0) diff --git a/authors.html b/authors.html index e85f44c..dd8460e 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ tximeta - 1.23.1 + 1.23.2

diff --git a/index.html b/index.html index e0d69ab..fb93856 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ tximeta - 1.23.1 + 1.23.2

diff --git a/news/index.html b/news/index.html index 314908f..b7e4cb4 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/pkgdown.yml b/pkgdown.yml index 32f2864..9224807 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.9 pkgdown_sha: ~ articles: tximeta: tximeta.html -last_built: 2024-05-14T14:49Z +last_built: 2024-06-08T13:08Z 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 380403c..f0de416 100644 --- a/reference/addCDS.html +++ b/reference/addCDS.html @@ -30,7 +30,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/reference/addExons.html b/reference/addExons.html index e3e3905..5f29a6c 100644 --- a/reference/addExons.html +++ b/reference/addExons.html @@ -25,7 +25,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/reference/addIds.html b/reference/addIds.html index b9ac69e..252b710 100644 --- a/reference/addIds.html +++ b/reference/addIds.html @@ -22,7 +22,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/reference/getTximetaBFC.html b/reference/getTximetaBFC.html index 174e455..63be27d 100644 --- a/reference/getTximetaBFC.html +++ b/reference/getTximetaBFC.html @@ -22,7 +22,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/reference/index.html b/reference/index.html index 8f8fe74..50af4e0 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/reference/linkedTxome.html b/reference/linkedTxome.html index 8f68732..b9182bc 100644 --- a/reference/linkedTxome.html +++ b/reference/linkedTxome.html @@ -23,7 +23,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/reference/makeDGEList.html b/reference/makeDGEList.html index fb09626..e6880fb 100644 --- a/reference/makeDGEList.html +++ b/reference/makeDGEList.html @@ -19,7 +19,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/reference/retrieveCDNA.html b/reference/retrieveCDNA.html index 4161f6e..1707046 100644 --- a/reference/retrieveCDNA.html +++ b/reference/retrieveCDNA.html @@ -22,7 +22,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/reference/retrieveDb.html b/reference/retrieveDb.html index 71230b8..c2f3775 100644 --- a/reference/retrieveDb.html +++ b/reference/retrieveDb.html @@ -21,7 +21,7 @@ tximeta - 1.23.1 + 1.23.2 @@ -115,11 +115,11 @@

Examples

#> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> loading existing TxDb created: 2024-05-14 14:50:17 +#> loading existing TxDb created: 2024-06-08 13:08:47 #> Loading required package: GenomicFeatures #> Loading required package: GenomeInfoDb #> Loading required package: GenomicRanges -#> loading existing transcript ranges created: 2024-05-14 14:50:18 +#> loading existing transcript ranges created: 2024-06-08 13:08:48 #> 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: 2024-05-14 14:50:17 +#> loading existing TxDb created: 2024-06-08 13:08:47 diff --git a/reference/splitSE.html b/reference/splitSE.html index 560ae2d..7e280b0 100644 --- a/reference/splitSE.html +++ b/reference/splitSE.html @@ -23,7 +23,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/reference/summarizeToGene.html b/reference/summarizeToGene.html index 22b3d84..30ac272 100644 --- a/reference/summarizeToGene.html +++ b/reference/summarizeToGene.html @@ -25,7 +25,7 @@ tximeta - 1.23.1 + 1.23.2 @@ -156,8 +156,8 @@

Examples

#> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> loading existing TxDb created: 2024-05-14 14:50:17 -#> loading existing transcript ranges created: 2024-05-14 14:50:18 +#> loading existing TxDb created: 2024-06-08 13:08:47 +#> loading existing transcript ranges created: 2024-06-08 13:08:48 #> Warning: #> #> Warning: the annotation is missing some transcripts that were quantified. @@ -178,10 +178,11 @@

Examples

#> tximet> #> tximet> gse <- summarizeToGene(se) -#> loading existing TxDb created: 2024-05-14 14:50:17 +#> loading existing TxDb created: 2024-06-08 13:08:47 #> obtaining transcript-to-gene mapping from database #> generating gene ranges -#> gene ranges assigned by total range of isoforms, see `assignRanges` +#> assignRanges='range': gene ranges assigned by total range of isoforms +#> see details at: ?summarizeToGene,SummarizedExperiment-method #> summarizing abundance #> summarizing counts #> summarizing length diff --git a/reference/tximeta-package.html b/reference/tximeta-package.html index e2d4667..e69c648 100644 --- a/reference/tximeta-package.html +++ b/reference/tximeta-package.html @@ -26,7 +26,7 @@ tximeta - 1.23.1 + 1.23.2 diff --git a/reference/tximeta.html b/reference/tximeta.html index 27d4b02..5a35257 100644 --- a/reference/tximeta.html +++ b/reference/tximeta.html @@ -21,7 +21,7 @@ tximeta - 1.23.1 + 1.23.2 @@ -222,8 +222,8 @@

Examples

#> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> loading existing TxDb created: 2024-05-14 14:50:17 -#> loading existing transcript ranges created: 2024-05-14 14:50:18 +#> loading existing TxDb created: 2024-06-08 13:08:47 +#> loading existing transcript ranges created: 2024-06-08 13:08:48 #> Warning: #> #> Warning: the annotation is missing some transcripts that were quantified.