more updates for pkgdown

.github/workflows/check-bioc.yml

@@ -73,9 +73,6 @@ jobs:
           mkdir /__w/_temp/Library
           echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
 
-      - name: work around permission issue
-        run: git config --global --add safe.directory /__w/nullranges/nullranges
-
       ## Most of these steps are the same as the ones in
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
@@ -185,15 +182,6 @@ jobs:
           # BiocManager::install("BiocCheck")
         shell: Rscript {0}
 
-      - name: Try downloading data
-        run: |
-          ## Attempt to download the data needed for vignette
-          library(nullrangesData)
-          dhs <- DHSA549Hg38()
-          bins <- hg19_10kb_bins()
-          binPairs <- hg19_10kb_ctcfBoundBinPairs()
-        shell: Rscript {0}
-
       - name: Install BiocGenerics
         if:  env.has_RUnit == 'true'
         run: |
@@ -287,7 +275,7 @@ jobs:
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: nullranges/nullranges
+          repository: thelovelab/tximeta
           tag_with_ref: true
           tag_with_sha: true
           tags: latest

R/tximeta.R

@@ -1,4 +1,4 @@
-#' Import transcript-level quantification data with automatic metadata
+#' Import transcript quantification with metadata
 #' 
 #' The tximeta package imports abundances (TPM), estimated counts,
 #' and effective lengths from Salmon, alevin, or other quantification
@@ -14,10 +14,9 @@
 #' The main functions are:
 #' \itemize{
 #' \item \code{\link{tximeta}} - with key argument: \code{coldata}
-#' \item \code{\link{summarizeToGene}} - summarize quants to gene-level
+#' \item \code{\link{summarizeToGene,SummarizedExperiment-method}} - summarize quants to gene-level
 #' \item \code{\link{retrieveDb}} - retrieve the transcript database
 #' \item \code{\link{addIds}} - add transcript or gene ID (see \code{gene} argument)
-#' \item \code{\link{addExons}} - convert from GRanges to GRangesList
 #' }
 #' 
 #' All software-related questions should be posted to the Bioconductor Support Site:
@@ -27,7 +26,7 @@
 #' The code can be viewed at the GitHub repository,
 #' which also lists the contributor code of conduct:
 #'
-#' \url{https://github.com/mikelove/tximeta}
+#' \url{https://github.com/thelovelab/tximeta}
 #' 
 #' @references
 #'
@@ -54,8 +53,8 @@
 #' @keywords package
 NULL
 
-#' tximeta: Transcript quantification import with automatic metadata
-#'
+#' Import transcript quantification with metadata
+#' 
 #' \code{tximeta} leverages the hashed checksum of the Salmon index,
 #' in addition to a number of core Bioconductor packages (GenomicFeatures,
 #' ensembldb, AnnotationHub, GenomeInfoDb, BiocFileCache) to automatically

pkgdown/_pkgdown.yml

@@ -20,15 +20,15 @@ reference:
     contents:
       - tximeta
       - starts_with("summarizeToGene")
-  - title: "Add info"
+  - title: "Add information to SE"
     contents:
       - starts_with("add")
-  - title: "linked"
-    contents:
-      - contains("linkedTxome")
-  - title: "Retrieve info"
+  - title: "Retrieve information from SE"
     contents:
       - starts_with("retrieve")
+  - title: "linkedTxome for custom transcriptomes"
+    contents:
+      - contains("linkedTxome")
   - title: "Other helpers"
     contents:
       - splitSE

vignettes/tximeta.Rmd

@@ -45,9 +45,9 @@ or to bundle one alevin output directory. For tips on using `tximeta`
 with other quantifiers see the 
 [other quantifiers](#other_quantifiers) section below.
 
-<center>
-<img width=600 src="diagram.png"/>
-</center>
+```{r echo=FALSE}
+knitr::include_graphics("images/diagram.png")
+```
 
 # Tximeta import starts with sample table