diff --git a/404.html b/404.html index 4894707..0fc0c3a 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 7f21b16..4503049 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/articles/index.html b/articles/index.html index ff8039b..dfbda3d 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/articles/tximeta.html b/articles/tximeta.html index ce5bbfa..11ca949 100644 --- a/articles/tximeta.html +++ b/articles/tximeta.html @@ -33,7 +33,7 @@ tximeta - 1.19.10 + 1.21.2 @@ -74,7 +74,7 @@

Tximeta: transcript quantification import with

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

-

10/09/2023

+

01/12/2024

Source: vignettes/tximeta.Rmd @@ -275,27 +275,27 @@

Pre-computed checksums GENCODE Homo sapiens -23-44 +23-45 GENCODE Mus musculus -M6-M33 +M6-M34 Ensembl Homo sapiens -76-110 +76-111 Ensembl Mus musculus -76-110 +76-111 Ensembl Drosophila melanogaster -79-110 +79-111 RefSeq @@ -404,7 +404,7 @@

Retrieve the transcript database -
## loading existing TxDb created: 2023-10-09 18:51:07
+
## loading existing TxDb created: 2024-01-12 13:23:25
## Loading required package: GenomicFeatures
## Loading required package: AnnotationDbi
@@ -439,7 +439,7 @@ 
Add exons per transcript
 
-
## loading existing TxDb created: 2023-10-09 18:51:07

+
## loading existing TxDb created: 2024-01-12 13:23:25

 
## generating exon ranges

 
 rowRanges(se.exons)[[1]]

@@ -478,7 +478,7 @@ 
Easy summarization to gene-leveltx_ids.

 
 gse <- summarizeToGene(se)

-
## loading existing TxDb created: 2023-10-09 18:51:07

+
## loading existing TxDb created: 2024-01-12 13:23:25

 
## obtaining transcript-to-gene mapping from database

 
## generating gene ranges

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

@@ -580,7 +580,7 @@ 
Differential expression analysisThe following code chunk demonstrates how to build a
 DESeqDataSet and begin a differential expression analysis.

 
-suppressPackageStartupMessages(library(DESeq2))
+suppressPackageStartupMessages(library(DESeq2))
 # here there is a single sample so we use ~1.
 # expect a warning that there is only a single sample...
 suppressWarnings({dds <- DESeqDataSet(gse, ~1)})

@@ -594,7 +594,7 @@ 
Differential expression analysistximeta
 if these were generated during quantification.

 
-library(fishpond)
+library(fishpond)
 y <- se
 # y <- scaleInfReps(y)
 # y <- labelKeep(y)
@@ -624,7 +624,7 @@ 
Differential expression analysis
 
 
## List of 3
 ##  $ version   :Classes 'package_version', 'numeric_version'  hidden list of 1
-##   ..$ : int [1:3] 1 19 10
+##   ..$ : int [1:3] 1 21 2
 ##  $ type      : chr "salmon"
-##  $ importTime: POSIXct[1:1], format: "2023-10-09 18:50:57"

+##  $ importTime: POSIXct[1:1], format: "2024-01-12 13:23:16"

 
 str(metadata(se)[["txdbInfo"]])

 
##  Named chr [1:13] "TxDb" "GenomicFeatures" ...
@@ -914,7 +914,7 @@ 
Linked transcriptomes                release="98", genome="BDGP6.22",
                 fasta=fastaFTP, gtf=gtfPath,
                 jsonFile=jsonFile)

-
## writing linkedTxome to /tmp/Rtmp0CoyeU/Dm.BDGP6.22.98.plus_salmon-0.14.1.json

+
## writing linkedTxome to /tmp/RtmpPFrOWi/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 checksum) with the sources is saved
@@ -1023,13 +1023,13 @@ 
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… 2023-10-09… 2023-10-09… /tmp… rela… 9296…                 NA NA   
-## 2 BFC2  Dros… 2023-10-09… 2023-10-09… /tmp… rela… 9296…                 NA NA   
-## 3 BFC3  txpR… 2023-10-09… 2023-10-09… /tmp… rela… 9292…                 NA NA   
-## 4 BFC4  exon… 2023-10-09… 2023-10-09… /tmp… rela… 9294…                 NA NA   
-## 5 BFC5  gene… 2023-10-09… 2023-10-09… /tmp… rela… 9293…                 NA NA   
-## 6 BFC6  Dros… 2023-10-09… 2023-10-09… /tmp… rela… 9294…                 NA NA   
-## 7 BFC7  txpR… 2023-10-09… 2023-10-09… /tmp… rela… 9293…                 NA NA   
+## 1 BFC1  link… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 2 BFC2  Dros… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 3 BFC3  txpR… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 4 BFC4  exon… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 5 BFC5  gene… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 6 BFC6  Dros… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 7 BFC7  txpR… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
 ## # ℹ 1 more variable: expires <dbl>
@@ -1072,8 +1072,8 @@

Loading linkedTxome JSON files< 
## 1 
 ## found matching linked transcriptome:
 ## [ LocalEnsembl - Drosophila melanogaster - release 98 ]
-## loading existing TxDb created: 2023-10-09 18:51:25
-## loading existing transcript ranges created: 2023-10-09 18:51:25
+## loading existing TxDb created: 2024-01-12 13:23:40 +## loading existing transcript ranges created: 2024-01-12 13:23:40 
## Warning in checkAssays2Txps(assays, txps): 
 ## 
 ## Warning: the annotation is missing some transcripts that were quantified.
@@ -1104,13 +1104,13 @@ 
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… 2023-10-09… 2023-10-09… /tmp… rela… 9296…                 NA NA   
-## 2 BFC3  txpR… 2023-10-09… 2023-10-09… /tmp… rela… 9292…                 NA NA   
-## 3 BFC4  exon… 2023-10-09… 2023-10-09… /tmp… rela… 9294…                 NA NA   
-## 4 BFC5  gene… 2023-10-09… 2023-10-09… /tmp… rela… 9293…                 NA NA   
-## 5 BFC6  Dros… 2023-10-09… 2023-10-09… /tmp… rela… 9294…                 NA NA   
-## 6 BFC7  txpR… 2023-10-09… 2023-10-09… /tmp… rela… 9293…                 NA NA   
-## 7 BFC8  link… 2023-10-09… 2023-10-09… /tmp… rela… 9297…                 NA NA   
+## 1 BFC2  Dros… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 2 BFC3  txpR… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 3 BFC4  exon… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 4 BFC5  gene… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 5 BFC6  Dros… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 6 BFC7  txpR… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
+## 7 BFC8  link… 2024-01-12… 2024-01-12… /tmp… rela… 1253…                 NA NA   
 ## # ℹ 1 more variable: expires <dbl>
@@ -1203,7 +1203,7 @@

Session infosession_info()

## ─ Session info ───────────────────────────────────────────────────────────────
 ##  setting  value
-##  version  R version 4.3.1 (2023-06-16)
+##  version  R version 4.3.2 (2023-10-31)
 ##  os       Ubuntu 22.04.3 LTS
 ##  system   x86_64, linux-gnu
 ##  ui       X11
@@ -1211,146 +1211,145 @@ 
Session info##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       UTC
-##  date     2023-10-09
+##  date     2024-01-12
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package                * version    date (UTC) lib source
 ##  abind                    1.4-5      2016-07-21 [1] RSPM (R 4.3.0)
-##  AnnotationDbi          * 1.62.2     2023-07-02 [1] Bioconductor
-##  AnnotationFilter         1.24.0     2023-04-25 [1] Bioconductor
-##  AnnotationHub            3.8.0      2023-04-25 [1] Bioconductor
-##  Biobase                * 2.60.0     2023-04-25 [1] Bioconductor
-##  BiocFileCache          * 2.8.0      2023-04-25 [1] Bioconductor
-##  BiocGenerics           * 0.46.0     2023-04-25 [1] Bioconductor
-##  BiocIO                   1.10.0     2023-04-25 [1] Bioconductor
-##  BiocManager              1.30.22    2023-08-08 [2] CRAN (R 4.3.1)
-##  BiocParallel             1.34.2     2023-05-22 [1] Bioconductor
-##  BiocVersion              3.17.1     2022-11-04 [2] Bioconductor
-##  biomaRt                  2.56.1     2023-06-09 [1] Bioconductor
-##  Biostrings               2.68.1     2023-05-16 [1] Bioconductor
+##  AnnotationDbi          * 1.64.1     2023-11-03 [1] Bioconductor
+##  AnnotationFilter         1.26.0     2023-10-24 [1] Bioconductor
+##  AnnotationHub            3.10.0     2023-10-24 [1] Bioconductor
+##  Biobase                * 2.62.0     2023-10-24 [1] Bioconductor
+##  BiocFileCache          * 2.10.1     2023-10-26 [1] Bioconductor
+##  BiocGenerics           * 0.48.1     2023-11-01 [1] Bioconductor
+##  BiocIO                   1.12.0     2023-10-24 [1] Bioconductor
+##  BiocManager              1.30.22    2023-08-08 [2] CRAN (R 4.3.2)
+##  BiocParallel             1.36.0     2023-10-24 [1] Bioconductor
+##  BiocVersion              3.18.1     2023-11-15 [2] Bioconductor
+##  biomaRt                  2.58.0     2023-10-24 [1] Bioconductor
+##  Biostrings               2.70.1     2023-10-25 [1] Bioconductor
 ##  bit                      4.0.5      2022-11-15 [1] RSPM (R 4.3.0)
 ##  bit64                    4.0.5      2020-08-30 [1] RSPM (R 4.3.0)
 ##  bitops                   1.0-7      2021-04-24 [1] RSPM (R 4.3.0)
 ##  blob                     1.2.4      2023-03-17 [1] RSPM (R 4.3.0)
-##  bslib                    0.5.1      2023-08-11 [2] RSPM (R 4.3.0)
+##  bslib                    0.6.1      2023-11-28 [2] RSPM (R 4.3.0)
 ##  cachem                   1.0.8      2023-05-01 [2] RSPM (R 4.3.0)
-##  callr                    3.7.3      2022-11-02 [2] RSPM (R 4.3.0)
-##  cli                      3.6.1      2023-03-23 [2] RSPM (R 4.3.0)
-##  codetools                0.2-19     2023-02-01 [3] CRAN (R 4.3.1)
+##  cli                      3.6.2      2023-12-11 [2] RSPM (R 4.3.0)
+##  codetools                0.2-19     2023-02-01 [3] CRAN (R 4.3.2)
 ##  colorspace               2.1-0      2023-01-23 [1] RSPM (R 4.3.0)
 ##  crayon                   1.5.2      2022-09-29 [2] RSPM (R 4.3.0)
-##  curl                     5.1.0      2023-10-02 [2] RSPM (R 4.3.0)
-##  DBI                      1.1.3      2022-06-18 [1] RSPM (R 4.3.0)
-##  dbplyr                 * 2.3.4      2023-09-26 [1] RSPM (R 4.3.0)
-##  DelayedArray             0.26.7     2023-07-28 [1] Bioconductor
-##  desc                     1.4.2      2022-09-08 [2] RSPM (R 4.3.0)
-##  DESeq2                 * 1.40.2     2023-06-23 [1] Bioconductor
+##  curl                     5.2.0      2023-12-08 [2] RSPM (R 4.3.0)
+##  DBI                      1.2.0      2023-12-21 [1] RSPM (R 4.3.0)
+##  dbplyr                 * 2.4.0      2023-10-26 [1] RSPM (R 4.3.0)
+##  DelayedArray             0.28.0     2023-10-24 [1] Bioconductor
+##  desc                     1.4.3      2023-12-10 [2] RSPM (R 4.3.0)
+##  DESeq2                 * 1.42.0     2023-10-24 [1] Bioconductor
 ##  devtools               * 2.4.5      2022-10-11 [2] RSPM (R 4.3.0)
 ##  digest                   0.6.33     2023-07-07 [2] RSPM (R 4.3.0)
-##  dplyr                    1.1.3      2023-09-03 [1] RSPM (R 4.3.0)
-##  edgeR                  * 3.42.4     2023-05-31 [1] Bioconductor
+##  dplyr                    1.1.4      2023-11-17 [1] RSPM (R 4.3.0)
+##  edgeR                  * 4.0.6      2024-01-08 [1] Bioconductor 3.18 (R 4.3.2)
 ##  ellipsis                 0.3.2      2021-04-29 [2] RSPM (R 4.3.0)
-##  ensembldb                2.24.1     2023-09-21 [1] Bioconductor
-##  evaluate                 0.22       2023-09-29 [2] RSPM (R 4.3.0)
-##  fansi                    1.0.5      2023-10-08 [2] RSPM (R 4.3.0)
+##  ensembldb                2.26.0     2023-10-24 [1] Bioconductor
+##  evaluate                 0.23       2023-11-01 [2] RSPM (R 4.3.0)
+##  fansi                    1.0.6      2023-12-08 [2] RSPM (R 4.3.0)
 ##  fastmap                  1.1.1      2023-02-24 [2] RSPM (R 4.3.0)
-##  filelock                 1.0.2      2018-10-05 [1] RSPM (R 4.3.0)
-##  fishpond               * 2.6.2      2023-06-19 [1] Bioconductor
+##  filelock                 1.0.3      2023-12-11 [1] RSPM (R 4.3.0)
+##  fishpond               * 2.8.0      2023-10-24 [1] Bioconductor
 ##  fs                       1.6.3      2023-07-20 [2] RSPM (R 4.3.0)
 ##  generics                 0.1.3      2022-07-05 [1] RSPM (R 4.3.0)
-##  GenomeInfoDb           * 1.36.4     2023-10-02 [1] Bioconductor
-##  GenomeInfoDbData         1.2.10     2023-08-25 [1] Bioconductor
-##  GenomicAlignments        1.36.0     2023-04-25 [1] Bioconductor
-##  GenomicFeatures        * 1.52.2     2023-08-25 [1] Bioconductor
-##  GenomicRanges          * 1.52.1     2023-10-08 [1] Bioconductor
-##  ggplot2                  3.4.3      2023-08-14 [1] RSPM (R 4.3.0)
+##  GenomeInfoDb           * 1.38.5     2023-12-28 [1] Bioconductor 3.18 (R 4.3.2)
+##  GenomeInfoDbData         1.2.11     2024-01-03 [1] Bioconductor
+##  GenomicAlignments        1.38.1     2024-01-08 [1] Bioconductor 3.18 (R 4.3.2)
+##  GenomicFeatures        * 1.54.1     2023-10-29 [1] Bioconductor
+##  GenomicRanges          * 1.54.1     2023-10-29 [1] Bioconductor
+##  ggplot2                  3.4.4      2023-10-12 [1] RSPM (R 4.3.0)
 ##  glue                     1.6.2      2022-02-24 [2] RSPM (R 4.3.0)
 ##  gtable                   0.3.4      2023-08-21 [1] RSPM (R 4.3.0)
-##  gtools                   3.9.4      2022-11-27 [1] RSPM (R 4.3.0)
+##  gtools                   3.9.5      2023-11-20 [1] RSPM (R 4.3.0)
+##  highr                    0.10       2022-12-22 [2] RSPM (R 4.3.0)
 ##  hms                      1.1.3      2023-03-21 [1] RSPM (R 4.3.0)
-##  htmltools                0.5.6.1    2023-10-06 [2] RSPM (R 4.3.0)
-##  htmlwidgets              1.6.2      2023-03-17 [2] RSPM (R 4.3.0)
-##  httpuv                   1.6.11     2023-05-11 [2] RSPM (R 4.3.0)
+##  htmltools                0.5.7      2023-11-03 [2] RSPM (R 4.3.0)
+##  htmlwidgets              1.6.4      2023-12-06 [2] RSPM (R 4.3.0)
+##  httpuv                   1.6.13     2023-12-06 [2] RSPM (R 4.3.0)
 ##  httr                     1.4.7      2023-08-15 [2] RSPM (R 4.3.0)
-##  interactiveDisplayBase   1.38.0     2023-04-25 [1] Bioconductor
-##  IRanges                * 2.34.1     2023-06-22 [1] Bioconductor
+##  interactiveDisplayBase   1.40.0     2023-10-24 [1] Bioconductor
+##  IRanges                * 2.36.0     2023-10-24 [1] Bioconductor
 ##  jquerylib                0.1.4      2021-04-26 [2] RSPM (R 4.3.0)
-##  jsonlite                 1.8.7      2023-06-29 [2] RSPM (R 4.3.0)
-##  KEGGREST                 1.40.1     2023-09-29 [1] Bioconductor
-##  knitr                    1.44       2023-09-11 [2] RSPM (R 4.3.0)
-##  later                    1.3.1      2023-05-02 [2] RSPM (R 4.3.0)
-##  lattice                  0.21-9     2023-10-01 [3] RSPM (R 4.3.0)
+##  jsonlite                 1.8.8      2023-12-04 [2] RSPM (R 4.3.0)
+##  KEGGREST                 1.42.0     2023-10-24 [1] Bioconductor
+##  knitr                    1.45       2023-10-30 [2] RSPM (R 4.3.0)
+##  later                    1.3.2      2023-12-06 [2] RSPM (R 4.3.0)
+##  lattice                  0.22-5     2023-10-24 [3] RSPM (R 4.3.0)
 ##  lazyeval                 0.2.2      2019-03-15 [1] RSPM (R 4.3.0)
-##  lifecycle                1.0.3      2022-10-07 [2] RSPM (R 4.3.0)
-##  limma                  * 3.56.2     2023-06-04 [1] Bioconductor
+##  lifecycle                1.0.4      2023-11-07 [2] RSPM (R 4.3.0)
+##  limma                  * 3.58.1     2023-10-31 [1] Bioconductor
 ##  locfit                   1.5-9.8    2023-06-11 [1] RSPM (R 4.3.0)
 ##  magrittr                 2.0.3      2022-03-30 [2] RSPM (R 4.3.0)
-##  Matrix                   1.6-1.1    2023-09-18 [3] RSPM (R 4.3.0)
-##  MatrixGenerics         * 1.12.3     2023-07-30 [1] Bioconductor
-##  matrixStats            * 1.0.0      2023-06-02 [1] RSPM (R 4.3.0)
+##  Matrix                   1.6-4      2023-11-30 [3] RSPM (R 4.3.0)
+##  MatrixGenerics         * 1.14.0     2023-10-24 [1] Bioconductor
+##  matrixStats            * 1.2.0      2023-12-11 [1] RSPM (R 4.3.0)
 ##  memoise                  2.0.1      2021-11-26 [2] RSPM (R 4.3.0)
 ##  mime                     0.12       2021-09-28 [2] RSPM (R 4.3.0)
 ##  miniUI                   0.1.1.1    2018-05-18 [2] RSPM (R 4.3.0)
 ##  munsell                  0.5.0      2018-06-12 [1] RSPM (R 4.3.0)
-##  org.Dm.eg.db           * 3.17.0     2023-08-25 [1] Bioconductor
+##  org.Dm.eg.db           * 3.18.0     2024-01-03 [1] Bioconductor
 ##  pillar                   1.9.0      2023-03-22 [2] RSPM (R 4.3.0)
-##  pkgbuild                 1.4.2      2023-06-26 [2] RSPM (R 4.3.0)
+##  pkgbuild                 1.4.3      2023-12-10 [2] RSPM (R 4.3.0)
 ##  pkgconfig                2.0.3      2019-09-22 [2] RSPM (R 4.3.0)
 ##  pkgdown                  2.0.7      2022-12-14 [2] RSPM (R 4.3.0)
 ##  pkgload                  1.3.3      2023-09-22 [2] RSPM (R 4.3.0)
 ##  png                      0.1-8      2022-11-29 [1] RSPM (R 4.3.0)
 ##  prettyunits              1.2.0      2023-09-24 [2] RSPM (R 4.3.0)
-##  processx                 3.8.2      2023-06-30 [2] RSPM (R 4.3.0)
 ##  profvis                  0.3.8      2023-05-02 [2] RSPM (R 4.3.0)
-##  progress                 1.2.2      2019-05-16 [1] RSPM (R 4.3.0)
+##  progress                 1.2.3      2023-12-06 [1] RSPM (R 4.3.0)
 ##  promises                 1.2.1      2023-08-10 [2] RSPM (R 4.3.0)
-##  ProtGenerics             1.32.0     2023-04-25 [1] Bioconductor
-##  ps                       1.7.5      2023-04-18 [2] RSPM (R 4.3.0)
+##  ProtGenerics             1.34.0     2023-10-24 [1] Bioconductor
 ##  purrr                    1.0.2      2023-08-10 [2] RSPM (R 4.3.0)
 ##  R6                       2.5.1      2021-08-19 [2] RSPM (R 4.3.0)
-##  ragg                     1.2.5      2023-01-12 [2] RSPM (R 4.3.0)
+##  ragg                     1.2.7      2023-12-11 [2] RSPM (R 4.3.0)
 ##  rappdirs                 0.3.3      2021-01-31 [2] RSPM (R 4.3.0)
 ##  Rcpp                     1.0.11     2023-07-06 [2] RSPM (R 4.3.0)
-##  RCurl                    1.98-1.12  2023-03-27 [1] RSPM (R 4.3.0)
-##  remotes                  2.4.2.9000 2023-10-06 [1] Github (r-lib/remotes@8875171)
-##  restfulr                 0.0.15     2022-06-16 [1] RSPM (R 4.3.0)
+##  RCurl                    1.98-1.13  2023-11-02 [1] RSPM (R 4.3.0)
+##  remotes                  2.4.2.9000 2024-01-12 [1] Github (r-lib/remotes@6fe8836)
+##  restfulr                 0.0.15     2022-06-16 [1] RSPM (R 4.3.2)
 ##  rjson                    0.2.21     2022-01-09 [1] RSPM (R 4.3.0)
-##  rlang                    1.1.1      2023-04-28 [2] RSPM (R 4.3.0)
+##  rlang                    1.1.2      2023-11-04 [2] RSPM (R 4.3.0)
 ##  rmarkdown                2.25       2023-09-18 [2] RSPM (R 4.3.0)
-##  rprojroot                2.0.3      2022-04-02 [2] RSPM (R 4.3.0)
-##  Rsamtools                2.16.0     2023-04-25 [1] Bioconductor
-##  RSQLite                  2.3.1      2023-04-03 [1] RSPM (R 4.3.0)
-##  rtracklayer              1.60.1     2023-08-15 [1] Bioconductor
-##  S4Arrays                 1.0.6      2023-08-30 [1] Bioconductor
-##  S4Vectors              * 0.38.2     2023-09-22 [1] Bioconductor
-##  sass                     0.4.7      2023-07-15 [2] RSPM (R 4.3.0)
-##  scales                   1.2.1      2022-08-20 [1] RSPM (R 4.3.0)
+##  Rsamtools                2.18.0     2023-10-24 [1] Bioconductor
+##  RSQLite                  2.3.4      2023-12-08 [1] RSPM (R 4.3.0)
+##  rtracklayer              1.62.0     2023-10-24 [1] Bioconductor
+##  S4Arrays                 1.2.0      2023-10-24 [1] Bioconductor
+##  S4Vectors              * 0.40.2     2023-11-23 [1] Bioconductor 3.18 (R 4.3.2)
+##  sass                     0.4.8      2023-12-06 [2] RSPM (R 4.3.0)
+##  scales                   1.3.0      2023-11-28 [1] RSPM (R 4.3.0)
 ##  sessioninfo              1.2.2      2021-12-06 [2] RSPM (R 4.3.0)
-##  shiny                    1.7.5      2023-08-12 [2] RSPM (R 4.3.0)
-##  SingleCellExperiment     1.22.0     2023-04-25 [1] Bioconductor
-##  stringi                  1.7.12     2023-01-11 [2] RSPM (R 4.3.0)
-##  stringr                  1.5.0      2022-12-02 [2] RSPM (R 4.3.0)
-##  SummarizedExperiment   * 1.30.2     2023-06-06 [1] Bioconductor
+##  shiny                    1.8.0      2023-11-17 [2] RSPM (R 4.3.0)
+##  SingleCellExperiment     1.24.0     2023-10-24 [1] Bioconductor
+##  SparseArray              1.2.3      2023-12-25 [1] Bioconductor 3.18 (R 4.3.2)
+##  statmod                  1.5.0      2023-01-06 [1] RSPM (R 4.3.0)
+##  stringi                  1.8.3      2023-12-11 [2] RSPM (R 4.3.0)
+##  stringr                  1.5.1      2023-11-14 [2] RSPM (R 4.3.0)
+##  SummarizedExperiment   * 1.32.0     2023-10-24 [1] Bioconductor
 ##  svMisc                   1.2.3      2021-10-11 [1] RSPM (R 4.3.0)
-##  systemfonts              1.0.4      2022-02-11 [2] RSPM (R 4.3.0)
-##  textshaping              0.3.6      2021-10-13 [2] RSPM (R 4.3.0)
+##  systemfonts              1.0.5      2023-10-09 [2] RSPM (R 4.3.0)
+##  textshaping              0.3.7      2023-10-09 [2] RSPM (R 4.3.0)
 ##  tibble                   3.2.1      2023-03-20 [2] RSPM (R 4.3.0)
 ##  tidyselect               1.2.0      2022-10-10 [1] RSPM (R 4.3.0)
-##  tximeta                * 1.19.10    2023-10-09 [1] Bioconductor
-##  tximport                 1.28.0     2023-04-25 [1] Bioconductor
+##  tximeta                * 1.21.2     2024-01-12 [1] Bioconductor
+##  tximport                 1.30.0     2023-10-24 [1] Bioconductor
 ##  urlchecker               1.0.1      2021-11-30 [2] RSPM (R 4.3.0)
 ##  usethis                * 2.2.2      2023-07-06 [2] RSPM (R 4.3.0)
-##  utf8                     1.2.3      2023-01-31 [2] RSPM (R 4.3.0)
-##  vctrs                    0.6.3      2023-06-14 [2] RSPM (R 4.3.0)
-##  withr                    2.5.1      2023-09-26 [2] RSPM (R 4.3.0)
-##  xfun                     0.40       2023-08-09 [2] RSPM (R 4.3.0)
-##  XML                      3.99-0.14  2023-03-19 [1] RSPM (R 4.3.0)
-##  xml2                     1.3.5      2023-07-06 [2] RSPM (R 4.3.0)
+##  utf8                     1.2.4      2023-10-22 [2] RSPM (R 4.3.0)
+##  vctrs                    0.6.5      2023-12-01 [2] RSPM (R 4.3.0)
+##  withr                    2.5.2      2023-10-30 [2] RSPM (R 4.3.0)
+##  xfun                     0.41       2023-11-01 [2] RSPM (R 4.3.0)
+##  XML                      3.99-0.16  2023-11-29 [1] RSPM (R 4.3.0)
+##  xml2                     1.3.6      2023-12-04 [2] RSPM (R 4.3.0)
 ##  xtable                   1.8-4      2019-04-21 [2] RSPM (R 4.3.0)
-##  XVector                  0.40.0     2023-04-25 [1] Bioconductor
-##  yaml                     2.3.7      2023-01-23 [2] RSPM (R 4.3.0)
-##  zlibbioc                 1.46.0     2023-04-25 [1] Bioconductor
+##  XVector                  0.42.0     2023-10-24 [1] Bioconductor
+##  yaml                     2.3.8      2023-12-11 [2] RSPM (R 4.3.0)
+##  zlibbioc                 1.48.0     2023-10-24 [1] Bioconductor
 ## 
 ##  [1] /__w/_temp/Library
 ##  [2] /usr/local/lib/R/site-library
diff --git a/authors.html b/authors.html
index d999ba9..6469e95 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       
       
         tximeta
-        1.19.10
+        1.21.2

diff --git a/index.html b/index.html index c495a59..4e288a8 100644 --- a/index.html +++ b/index.html @@ -37,7 +37,7 @@ tximeta - 1.19.10 + 1.21.2
diff --git a/news/index.html b/news/index.html index 9edf021..56bbecd 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ tximeta - 1.19.10 + 1.21.2 @@ -50,6 +50,10 @@

Changelog

Source: NEWS.md +
+

tximeta 1.21.2

+
  • GENCODE 44 (H.s.), M34 (M.m), and Ensembl 111
    • +

tximeta 1.20.0

  • Add argument to summarizeToGene(): assignRanges that takes either “range” (default) or “abundant”, and determines the ranges that are attached to the SE (rowRanges). Note that this new argument does not affect the data aggregation at all (counts and abundance are summarized to gene by tximport). The default behavior of summarizeToGene() returns ranges that correspond to the range of the isoforms of the gene, that is the leftmost basepair to the rightmost basepair of any isoform. The non-default “abundant” instead returns the range of the most abundant isoform in the data, averaging over samples. Information about the choice of range is included in mcols diff --git a/pkgdown.yml b/pkgdown.yml index 7fd43fc..588da55 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: tximeta: tximeta.html -last_built: 2023-10-09T18:50Z +last_built: 2024-01-12T13:22Z 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 4fad316..92652cb 100644 --- a/reference/addCDS.html +++ b/reference/addCDS.html @@ -30,7 +30,7 @@ tximeta - 1.19.10 + 1.21.2
diff --git a/reference/addExons.html b/reference/addExons.html index 0819874..912f4ed 100644 --- a/reference/addExons.html +++ b/reference/addExons.html @@ -25,7 +25,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/reference/addIds.html b/reference/addIds.html index 81b802e..47a79d6 100644 --- a/reference/addIds.html +++ b/reference/addIds.html @@ -22,7 +22,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/reference/getTximetaBFC.html b/reference/getTximetaBFC.html index 5b7e793..958d29f 100644 --- a/reference/getTximetaBFC.html +++ b/reference/getTximetaBFC.html @@ -22,7 +22,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/reference/index.html b/reference/index.html index 7912ca2..9e83e4e 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/reference/linkedTxome.html b/reference/linkedTxome.html index 159330e..f2fc672 100644 --- a/reference/linkedTxome.html +++ b/reference/linkedTxome.html @@ -23,7 +23,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/reference/makeDGEList.html b/reference/makeDGEList.html index 9273209..0978cac 100644 --- a/reference/makeDGEList.html +++ b/reference/makeDGEList.html @@ -19,7 +19,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/reference/retrieveCDNA.html b/reference/retrieveCDNA.html index f66e1b4..d908126 100644 --- a/reference/retrieveCDNA.html +++ b/reference/retrieveCDNA.html @@ -22,7 +22,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/reference/retrieveDb.html b/reference/retrieveDb.html index a9272ca..9e098a7 100644 --- a/reference/retrieveDb.html +++ b/reference/retrieveDb.html @@ -21,7 +21,7 @@ tximeta - 1.19.10 + 1.21.2 @@ -115,11 +115,11 @@

Examples

#> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> loading existing TxDb created: 2023-10-09 18:50:37 +#> loading existing TxDb created: 2024-01-12 13:22:59 #> Loading required package: GenomicFeatures #> Loading required package: GenomeInfoDb #> Loading required package: GenomicRanges -#> loading existing transcript ranges created: 2023-10-09 18:50:37 +#> loading existing transcript ranges created: 2024-01-12 13:22:59 #> 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: 2023-10-09 18:50:37 +#> loading existing TxDb created: 2024-01-12 13:22:59 diff --git a/reference/splitSE.html b/reference/splitSE.html index 78bd337..33a7494 100644 --- a/reference/splitSE.html +++ b/reference/splitSE.html @@ -23,7 +23,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/reference/summarizeToGene.html b/reference/summarizeToGene.html index bfa3dac..c6556f6 100644 --- a/reference/summarizeToGene.html +++ b/reference/summarizeToGene.html @@ -25,7 +25,7 @@ tximeta - 1.19.10 + 1.21.2 @@ -156,8 +156,8 @@

Examples

#> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> loading existing TxDb created: 2023-10-09 18:50:37 -#> loading existing transcript ranges created: 2023-10-09 18:50:37 +#> loading existing TxDb created: 2024-01-12 13:22:59 +#> loading existing transcript ranges created: 2024-01-12 13:22:59 #> 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: 2023-10-09 18:50:37 +#> loading existing TxDb created: 2024-01-12 13:22:59 #> obtaining transcript-to-gene mapping from database #> generating gene ranges #> gene ranges assigned by total range of isoforms, see `assignRanges` diff --git a/reference/tximeta-package.html b/reference/tximeta-package.html index 4fdcd23..b47b93a 100644 --- a/reference/tximeta-package.html +++ b/reference/tximeta-package.html @@ -26,7 +26,7 @@ tximeta - 1.19.10 + 1.21.2 diff --git a/reference/tximeta.html b/reference/tximeta.html index de60e9c..59fdf0e 100644 --- a/reference/tximeta.html +++ b/reference/tximeta.html @@ -21,7 +21,7 @@ tximeta - 1.19.10 + 1.21.2 @@ -222,8 +222,8 @@

Examples

#> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> loading existing TxDb created: 2023-10-09 18:50:37 -#> loading existing transcript ranges created: 2023-10-09 18:50:37 +#> loading existing TxDb created: 2024-01-12 13:22:59 +#> loading existing transcript ranges created: 2024-01-12 13:22:59 #> Warning: #> #> Warning: the annotation is missing some transcripts that were quantified.