Changes in version 1.20.3
- GENCODE 44 (H.s.), M34 (M.m), and Ensembl 111
- RefSeq p13 for human, p6 for mouse
Changes in version 1.20.0
- Add argument to summarizeToGene(): assignRanges that takes either
"range" (default) or "abundant", and determines the ranges that are
attached to the SE (rowRanges). Note that this new argument does not
affect the data aggregation at all (counts and abundance are
summarized to gene by tximport). The default behavior of
summarizeToGene() returns ranges that correspond to the range of the
isoforms of the gene, that is the leftmost basepair to the rightmost
basepair of any isoform. The non-default "abundant" instead returns
the range of the most abundant isoform in the data, averaging over
samples. Information about the choice of range is included in mcols
- Added support for piscem-infer: type="piscem" also auto-detected
from file ending.
Changes in version 1.19.8
- Added support for piscem-infer: type="piscem" also auto-detected
from file ending.
Changes in version 1.19.6
- Fixed genome build for mouse M26 and higher to GRCm39, thanks to
Charlotte Soneson.
Changes in version 1.14.0
- Allow GTF specification in linkedTxome to be a serialized GRanges
file (a file path to a .rda or .RData file). This bypasses some
apparent issue where makeTxDbFromGFF fails while makeTxDbFromGRanges
works.
- Up to GENCODE 40 (H.s.), M29 (M.m), and Ensembl 106
Changes in version 1.10.0
- Added more tximeta() messaging about specifying the 'source' in
linkedTxome. Essentially, this triggers GTF processing behavior that
users may want to avoid, and so specifying a string other than
"Ensembl" may be preferred. Also added note to vignette.
- Added note to vignette about alevin import with tximeta where the
'tgMap' step requires gene IDs and not gene symbols.
- Added hashes for: GENCODE 38 (H.s.), M27 (M.m), and Ensembl 104;
GENCODE 37 (H.s.), M26 (M.m), and Ensembl 103; GENCODE 36 and
Ensembl 102.
- Fixed a bug around AnnotationHub pulldown when using RefSeq as the
source.
- Fixed a bug where multiple parsed Ensembl GTF TxDb would be added to
the BiocFileCache with the same rname.
Changes in version 1.8.0
- Added 'fromDb' argument to addIds() to allow IDs to be added from
the associated TxDb/EnsDb instead of the org package (which is used
by default). Feature suggestion from Kristoffer Vitting-Seerup.
- Added function retrieveCDNA() that will download or load a cached
version of the transcript sequences used for quantification. Note
that the returned sequences are not ordered or matched to the rows
of the SummarizedExperiment object. Feature suggestion from
Kristoffer Vitting-Seerup.
- Added function addCDS() that will add CDS ranges for coding
transcripts (and fills in original ranges for non-coding), as well
as a 'coding' column as a logical indicator. Feature suggestion from
Kristoffer Vitting-Seerup.
- Added option that environmental variable TXIMETA_HUB_CACHE can be
used to set tximeta's cache location, to avoid prompting the user on
the first run of tximeta().
- tximeta() will now pull GENCODE TxDb from AnnotationHub when it is
listed there (only Homo sapiens are at this point in time). Thanks
to Leonardo Collado-Torres for the suggestion!
- Now summarizeToGene() will add a column tx_ids, which is a
CharacterList of the transcript IDs.
Changes in version 1.6.0
- Added PLOS Computational Biology citation! :-)
- Added function splitSE to split one assay of a SummarizedExperiment
into multiple assays, each containing features of a given type.
- Added a wrapper function makeDGEList() to simplify making a DGEList
for use with edgeR. See vignette for example.
- tximeta will now make use of EnsDb created and distributed on
AnnotationHub, unless useHub=FALSE. Also, a new function
retrieveDb() can be called on a SummarizedExperiment to retrieve the
underlying TxDb or EnsDb.
- tximeta can now use customMetaInfo argument to locate a custom
metadata information file such as meta_info.json, which should
contain a tage, index_seq_hash, with the SHA-256 hash value of the
reference transcripts.
- Added markDuplicateTxps argument to add hasDuplicate and duplicates
columns to rowData of SummarizedExperiment. One note is that, for
efficiency, this argument and cleanDuplicateTxps will now share a
duplicates CharacterList that is stored in the BiocFileCache, with
the name dups-.... Therefore, if you have previously used
cleanDuplicateTxps, you may need to bfcremove() any dups-...
entries. Summarization to gene level will keep track of numDupSets
per gene which informs about the number of transcripts sets
(equivalence classes by transcript sequence content).
- If during the indexing step, user didn't use --gencode for a Gencode
transcriptome file, tximeta will deal with this internally now by
stripping all characters after the vertical bar |, in order to match
long transcript names in the quant.sf files to the correct
transcript names in the GTF.
Changes in version 1.4.0
- tximeta will now pull down RefSeq seqinfo, using the dirname() of
the GTF location, and assuming some consistency in the structure of
the assembly_report.txt that is located in the same directory. Needs
more testing though across releases and organisms.
- expanded caching of ranges to exons and genes as well. Exons in
particular take a long time to build from TxDb, so this saves quite
a lot of time.
- new 'addExons' function will add exons to trancript-level summarized
experiments, by replacing transcript GRanges with exon-by-transcript
GRangesList. Purposely designed only for transcript-level, see note
in ?addExons
- tximeta now also caches the transcript ranges themselves, rather
than just the TxDb. This shaves extra seconds off the tximeta()
call!
- add 'skipSeqinfo' argument, which avoids attempting to fetch
chromosome information (from UCSC) if set to TRUE.
Changes in version 1.2.0
- Specifying gene=TRUE in addIds() when rows are transcripts will
attempt to use a gene_id column to map the IDs. This usually gives a
better mapping rate.
- Cut off version number from Ensembl names only (not GENCODE)
- Added 'cleanDuplicateTxps' argument, which does a lot of work for
the user: it downloads the FASTA from the source, identifies
duplicate transcripts (identical cDNA sequence) then looks to see if
transcripts that are in the quantification files, but missing from
the GTF, could be renamed from the list of duplicate transcripts
such that they would be present in the GTF.
- Added coding * non-coding combinations of Ensembl transcriptomes to
the hash table. Must be in this order: coding, then non-coding.
- Added support for dammit de novo transcriptomes.
- Added summarizeToGene as a method, to avoid conflicts with tximport.
- Added in Charlotte's code to split out GENCODE and Ensembl code for
generating transcript ranges.