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r-bioc-tximport 1.18.0%2Bdfsg-1
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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.