clarify piscem infer details

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: tximeta
-Version: 1.19.9
+Version: 1.19.10
 Title: Transcript Quantification Import with Automatic Metadata
 Description: Transcript quantification import from Salmon and
-    alevin with automatic attachment of transcript ranges and
-    release information, and other associated metadata. De novo
+    other quantifiers with automatic attachment of transcript ranges
+    and release information, and other associated metadata. De novo
     transcriptomes can be linked to the appropriate sources with
     linkedTxomes and shared for computational reproducibility.
 Authors@R: c(

R/tximeta.R

@@ -55,13 +55,11 @@ NULL
 
 #' Import transcript quantification with metadata
 #' 
-#' \code{tximeta} leverages the hashed checksum of the Salmon index,
+#' \code{tximeta} leverages the hashed checksum of the Salmon or piscem index,
 #' in addition to a number of core Bioconductor packages (GenomicFeatures,
 #' ensembldb, AnnotationHub, GenomeInfoDb, BiocFileCache) to automatically
 #' populate metadata for the user, without additional effort from the user.
-#' Note that \code{tximeta} requires that the entire output directory of Salmon
-#' or alevin is present and unmodified in order to identify the provenance of the
-#' reference transcripts.
+#' For other quantifiers see the \code{customMetaInfo} argument below.
 #'
 #' Most of the code in \code{tximeta} works to add metadata and transcript ranges
 #' when the quantification was performed with Salmon. However,

README.md

@@ -9,7 +9,12 @@ metadata for transcript quantification data in Bioconductor. The
 `tximeta()` function imports quantification data from *Salmon* or
 other quantifiers, and returns a 
 [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html#anatomy-of-a-summarizedexperiment)
-object.
+object. *tximeta* works natively with 
+[Salmon](https://salmon.readthedocs.io/en/latest/),
+[alevin](https://salmon.readthedocs.io/en/latest/alevin.html),
+or [piscem-infer](https://piscem-infer.readthedocs.io/en/latest/),
+but can easily be configured to work with any transcript
+quantification tool.
 
 If `tximeta()` recognizes the reference transcripts used
 for quantification, it will automatically download relevant
@@ -31,12 +36,14 @@ quantification data).
 
 # How it works
 
-The key idea behind *tximeta* is that *Salmon* propagates a hash value
+The key idea behind *tximeta* is that *Salmon*, *alevin*, and
+*piscem-infer* propagate a hash value
 summarizing the reference transcripts into each quantification
 directory it outputs. *tximeta* can be used with other tools as long
 as the 
 [hash of the transcripts](https://github.com/COMBINE-lab/FastaDigest) 
-is also included in the output directories. 
+is also included in the output directories. See `customMetaInfo`
+argument of `tximeta()` for more details.
 
 ![](man/figures/diagram.png)
 

vignettes/tximeta.Rmd

@@ -10,9 +10,9 @@ output:
 abstract: >
   Tximeta performs numerous annotation and metadata gathering tasks on
   behalf of users during the import of transcript quantifications from
-  *Salmon* or *alevin* into R/Bioconductor. Metadata and transcript
-  ranges are added automatically, facilitating genomic analyses and
-  assisting in computational reproducibility.
+  *Salmon*, *alevin*, or *piscem-infer* into R/Bioconductor. Metadata 
+  and transcript ranges are added automatically, facilitating genomic 
+  analyses and assisting in computational reproducibility.
 bibliography: library.bib
 vignette: |
   %\VignetteIndexEntry{Transcript quantification import with automatic metadata}
@@ -25,7 +25,8 @@ vignette: |
 The `tximeta` package [@Love2020] extends the `tximport` package
 [@Soneson2015] for import of transcript-level quantification data into
 R/Bioconductor. It automatically adds annotation metadata when the
-RNA-seq data has been quantified with *Salmon* [@Patro2017] or for
+RNA-seq data has been quantified with *Salmon* [@Patro2017] or 
+[piscem-infer](https://piscem-infer.readthedocs.io/en/latest/), or the
 scRNA-seq data quantified with *alevin* [@Srivastava2019]. To our
 knowledge, `tximeta` is the only package for RNA-seq data import that
 can automatically identify and attach transcriptome metadata based on
@@ -34,15 +35,15 @@ For more details on these packages -- including the motivation for
 `tximeta` and description of similar work -- consult the
 **References** below.
 
-**Note:** `tximeta` requires that the **entire output directory** of
-*Salmon* / *alevin* is present and unmodified in order to identify the
-provenance of the reference transcripts. In general, it's a good idea
-to not modify or re-arrange the output directory of bioinformatic
-software as other downstream software rely on and assume a consistent
-directory structure. For sharing multiple samples, one can use, for
-example, `tar -czf` to bundle up a set of Salmon output directories,
-or to bundle one alevin output directory. For tips on using `tximeta`
-with other quantifiers see the 
+**Note:** `tximeta` requires that the **entire output** of
+*Salmon* / *piscem-infer* / *alevin* is present and unmodified in
+order to identify the provenance of the reference transcripts. In
+general, it's a good idea to not modify or re-arrange the output
+directory of bioinformatic software as other downstream software rely
+on and assume a consistent directory structure. For sharing multiple
+samples, one can use, for example, `tar -czf` to bundle up a set of
+Salmon output directories, or to bundle one alevin output
+directory. For tips on using `tximeta` with other quantifiers see the
 [other quantifiers](#other_quantifiers) section below.
 
 ```{r echo=FALSE}