CHANGES IN VERSION 1.19.4
-------------------------
o 'ignoreAfterBar' and txOut=TRUE will now strip the characters
after '|' on the rownames of the output matrices.
CHANGES IN VERSION 1.18.0
-------------------------
o Code cleanup for deprecated functions. tximport reads in
only alevin version 0.14.0 or greater. For older data, use
previous versions of tximport.
CHANGES IN VERSION 1.16.0
------------------------
o Moved alevin arguments into a new 'list' argument, alevinArgs.
As of this version the possible values for alevinArgs are:
filterBarcodes, tierImport, forceSlow (all logical).
o Added alevinArgs argument `tierImport`, which will import
the "tier" information from alevin on the quantification
assessment.
o Add an alevinArgs argument `filterBarcodes`, which will only
import cells with barcodes in the `whitelist.txt` file.
o Fixed bug where the bootstrap matrices from alevin were
not aligned by cell with the counts matrix. This affected the
variance and the infReps list. The fix will also be
propogated to tximport v1.14.1 (Oct 2019 release).
CHANGES IN VERSION 1.15.12
--------------------------
o Moved alevin arguments into a new 'list' argument, alevinArgs.
As of this version the possible values for alevinArgs are:
filterBarcodes, tierImport, forceSlow (all logical).
o Added alevinArgs argument `tierImport`, which will import
the "tier" information from alevin on the quantification
assessment.
CHANGES IN VERSION 1.15.10
--------------------------
o Add an alevinArgs argument `filterBarcodes`, which will only
import cells with barcodes in the `whitelist.txt` file.
CHANGES IN VERSION 1.15.9
-------------------------
o Fixed bug where the bootstrap matrices from alevin were
not aligned by cell with the counts matrix. This affected the
variance and the infReps list. The fix will also be
propogated to tximport v1.14.1 (Oct 2019 release).
CHANGES IN VERSION 1.14.0
--------------------------
o alevin count and inferential variance can be imported now
~40x faster for large number of cells, leveraging C++ code
from the fishpond package (>= 1.1.18).
o alevin inferential replicates can be imported (also sparse).
To not import the inferential replicates, set dropInfReps=TRUE.
CHANGES IN VERSION 1.11.1
-------------------------
o Added argument 'sparse' and 'sparseThreshold' to allow for
sparse count import. For the initial implemenation:
only works for txOut=TRUE; countsFromAbundance either "no"
or "scaledTPM"; doesn't work with inferential replicates,
and only imports counts (and abundances if
countsFromAbundance="scaledTPM").
CHANGES IN VERSION 1.9.11
-------------------------
o Exporting simple internal function makeCountsFromAbundance().
CHANGES IN VERSION 1.9.10
-------------------------
o Added 'infRepStat' argument which offers re-compution
of counts and abundances using a function applied to the
inferential replicates, e.g. matrixStats::rowMedian for
using the median of posterior samples as the point estimate
provided in "counts" and "abundance". If 'countsFromAbundance'
is specified, this will compute counts a second time from
the re-computed abundances.
CHANGES IN VERSION 1.9.9
------------------------
o Adding support for gene-level summarization of inferential
replicates. This takes place by perform row summarization
on the inferential replicate (counts) in the same manner
as the original counts (and optionally computing the variance).
CHANGES IN VERSION 1.9.6
------------------------
o Added new countsFromAbundance method: "dtuScaledTPM".
This is designed for DTU analysis and to be used with txOut=TRUE.
It provides counts that are scaled, with a gene, by the median
transcript length among isoforms, then later by the sample's
sequencing depth, as in the other two methods.
The transcript lengths are calculated by first taking the
average across samples. With this new method, all the abundances
within a gene across all samples are scaled up by the same
length, preserving isoform proportions calculated from the counts.
CHANGES IN VERSION 1.9.4
------------------------
o Made a change to summarizeToGene() that will now provide
different output with a warning to alert the user.
The case is: if tximport() is run with countsFromAbundance="scaledTPM"
or "lengthScaledTPM" and txOut=TRUE, followed by
summarizeToGene() with countsFromAbundance="no".
This is a problematic series of calls, and previously
it was ignoring the fact that the incoming counts are
not original counts. Now, summarizeToGene() will throw
a warning and override countsFromAbundance="no" to
instead set it to the value that was used when tximport
was originally run, either "scaledTPM" or "lengthScaledTPM".
CHANGES IN VERSION 1.9.1
------------------------
o Fixed edgeR example code in vignette to use scaleOffset
after recommendation from Aaron Lun (2018-05-25).
CHANGES IN VERSION 1.8.0
------------------------
o Added support for StringTie output.
CHANGES IN VERSION 1.3.8
------------------------
o Support for inferential replicates written
by Rob Patro! Works for Salmon, Sailfish
and kallisto. See details in ?tximport.
CHANGES IN VERSION 1.3.6
------------------------
o Now, 'countsFromAbundance' not ignored when txOut=TRUE.
CHANGES IN VERSION 1.3.4
------------------------
o Support for kallisto HDF5 files thanks to
Andrew Parker Morgan and Ryan C Thompson
o Removing 'reader' argument, leaving only
'importer' argument. In addition, read_tsv
will be used by default if readr package is
installed.
o Messages from the importing function are
captured to avoid screen clutter.
CHANGES IN VERSION 0.99.0
-------------------------
o Preparing package for Bioconductor submission.
CHANGES IN VERSION 0.0.19
-------------------------
o Added `summarizeToGene` which breaks out the gene-level
summary step, so it can be run by users on lists of
transcript-level matrices produced by `tximport` with
`txOut=TRUE`.
CHANGES IN VERSION 0.0.18
=========================
o Changed argument `gene2tx` to `tx2gene`.
This order is more intuitive: linking transcripts to genes,
and matches the `geneMap` argument of Salmon and Sailfish.