NEWS

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tximport 1.31.1

• Experimental support for oarfish. At this point we are importing number of reads as both 'abundance' and 'counts'.

tximport 1.30.0

• Support for piscem-infer: use 'type="piscem"'.

tximport 1.27.1

• Changing license from GPL to LGPL.

tximport 1.25.1

• Now the 'eds' package exports readEDS() instead of 'fishpond'.

tximport 1.19.4

• 'ignoreAfterBar' and txOut=TRUE will now strip the characters after '|' on the rownames of the output matrices.

tximport 1.18.0

• Code cleanup for deprecated functions. tximport reads in only alevin version 0.14.0 or greater. For older data, use previous versions of tximport.

tximport 1.16.0

• Moved alevin arguments into a new 'list' argument, alevinArgs. As of this version the possible values for alevinArgs are: filterBarcodes, tierImport, forceSlow (all logical).
• Added alevinArgs argument 'tierImport', which will import the "tier" information from alevin on the quantification assessment.
• Add an alevinArgs argument 'filterBarcodes', which will only import cells with barcodes in the 'whitelist.txt' file.
• 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).

tximport 1.15.12

• Moved alevin arguments into a new 'list' argument, alevinArgs. As of this version the possible values for alevinArgs are: filterBarcodes, tierImport, forceSlow (all logical).
• Added alevinArgs argument 'tierImport', which will import the "tier" information from alevin on the quantification assessment.

tximport 1.15.10

• Add an alevinArgs argument 'filterBarcodes', which will only import cells with barcodes in the 'whitelist.txt' file.

tximport 1.15.9

• 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).

tximport 1.14.0

• 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).
• alevin inferential replicates can be imported (also sparse). To not import the inferential replicates, set dropInfReps=TRUE.

tximport 1.11.1

• 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").

tximport 1.9.11

• Exporting simple internal function makeCountsFromAbundance().

tximport 1.9.10

• 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.

tximport 1.9.9

• 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).

tximport 1.9.6

• 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.

tximport 1.9.4

• 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".

tximport 1.9.1

• Fixed edgeR example code in vignette to use scaleOffset after recommendation from Aaron Lun (2018-05-25).

tximport 1.8.0

• Added support for StringTie output.

tximport 1.3.8

• Support for inferential replicates written by Rob Patro! Works for Salmon, Sailfish and kallisto. See details in ?tximport.

tximport 1.3.6

• Now, 'countsFromAbundance' not ignored when txOut=TRUE.

tximport 1.3.4

• Support for kallisto HDF5 files thanks to Andrew Parker Morgan and Ryan C Thompson
• Removing 'reader' argument, leaving only 'importer' argument. In addition, read_tsv will be used by default if readr package is installed.
• Messages from the importing function are captured to avoid screen clutter.

tximport 0.99.0

• Preparing package for Bioconductor submission.

tximport 0.0.19

• 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'.

tximport 0.0.18

• Changed argument 'gene2tx' to 'tx2gene'. This order is more intuitive: linking transcripts to genes, and matches the 'geneMap' argument of Salmon and Sailfish.