Make good use of \VignetteIndexEntry to get vignettes listed in right order
 

 bump version
 

 Update droplet-processing.Rmd and protein-abundance.Rmd

- `scRNAseq::StoeckiusHashingData()` and `scRNAseq::KotliarovPBMCData()` again produce an SCE with altExp stored as SCE rather than SE
  - See https://github.com/LTLA/scRNAseq/issues/49#issuecomment-2065871509 and https://github.com/LTLA/scRNAseq/commit/2b0b5ea1c5960482b62a3b3fff1106172c58e873
- Also revert unintentional change (committed in f20d141) to use of serial instead of parallel processing with `computeCorrelations()` and `findTopCorrelations()` in in protein-abundance.Rmd
 

 Bump minimum version of scRNAseq dependency
 

 update NEWS file
 

 version bump 1.29.1
 

 use "_PACKAGE" for roxygen
 

 version bump 1.17.1
 

 update NEWS file
 

 bump version to 1.5.2
 

 Fix for Clang 16

See https://github.com/Bioconductor/SparseArray/issues/9

Note on previous commit: commit 2fc4998 added back and forth coersions
between ngCMatrix and SVT_SparseMatrix objects.
 

 Merge pull request #120 from sanchit-saini/ucsc-web-testcases

Add test cases to check if the UCSC scraping logic works properly 

 Add testcases for more functions
 

 Fixed issue with torch library (#70)

When the torch library has not been fully installed
the code was throwing an error

Moved all torch loading code into a separate utility function 

 Updated vignette with the new link_data parameter.
 

 Fix the issue for importMatrix when 'w' is missing.
 

 bump to version 1.13.1
 

 Update check-bioc.yml
 

 add batch2 and ... as arguments in batchCorrectionAssay
 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 Bioconductor 3.20 devel
 

 Bioconductor 3.19 release
 

 Merge remote-tracking branch 'upstream/devel' into devel

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_19 branch
 

 Merge remote-tracking branch 'upstream/RELEASE_3_19' into devel

* upstream/RELEASE_3_19:
  bump x.y.z version to even y prior to creation of RELEASE_3_19 branch
 

 Fixed reading when Inf is present
 

 fix gsva API update
 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 citecontact_1.3.1
 

 citecontact_1.1.1
 

 added TOMFlowPlot
 

 Minor fixes
 

 bump version to 1.5.1
 

 Version bump after bugfix
 

 Bump SVT_VERSION from 0 to 1

The layout of the Sparse Vector Tree (SVT) used in SVT_SparseArray objects
is now versioned, and internal global variable SVT_VERSION keeps track of
that.
In SVT_VERSION 1, the order of the nzvals/nzoffs components in the SVT
leaves is switched w.r.t. SVT_VERSION 0: new order is nzvals/nzoffs;
previous order was nzoffs/nzvals.
Version 0 was used in SparseArray < 1.5.0. This means that SVT_SparseArray
objects created and serialized with SparseArray < 1.5.0 are not compatible
with SparseArray >= 1.5.0 for now. An updateObject() method might be added
later.
 

 fix to contrast output column names in vignette
 

 test for empty output
 

 Increment version
 

 bump version
 

 Merge branch 'devel' into RELEASE_3_19
 

 bump version to test gitactions
 

 update news
 

 add segtoFreq function
 

 Fix track(UCSCSession) to retrieve track by table Name
 

 Fix duplicate title in README
 

 usethis::use_logo("~/Desktop/TREG_logo/TREG_logo.png")
 

 Change argname1 and 2 in the documentation to arg_name1 and arg_name2
 

 add documentation for check_tx_names

Co-authored-by: Nick Eagles <nickeagles77@gmail.com>
 

 Update NEWS
 

 Add a check and a unit test to validate rse_tx as an rse object
 

 Update the NEWS for the version 1.7.0
 

 Change qsvaR::degradation_tstats to deg_tstats
 

 Add a check and unit test for input to be an rse object

Co-authored-by: Nick Eagles <nickeagles77@gmail.com>
 

 Add warning message to the unit test

Co-authored-by: Nick Eagles <nickeagles77@gmail.com>
 

 Switch order to check if rse_tx is an rse object first
 

 Update the unit test output is a ggplot
 

 Change null to capital NULL
 

 Combine the unit test to check if output is a matrix
 

 Update example for get_qsvs function
 

 Add single quote to the qsvsPCs in the error message
 

 make the check for k isn't zero after validate qsvPCs is a prcomp object
 

 Change RSE by array and add unit test for k higher than ncol
 

 Add unit test to throw an error if assayname is in assayNames
 

 Add unit test for assayname not in assayNames
 

 Add unit test for assayname not in assayNames
 

 Break the line and add call.=False
 

 Add rownames for the intersection between deg_tstats and DE
 

 Remove unit test for None of the DE rownames are in degradation_tstats rownames
 

 Fix the error message
 

 Remove unit test for test where none of the sig_transcripts are in rse_tx rownames
 

 Add a single quote
 

 Add unit test for mixed GENCODE and ENSEMBL annotation

Co-authored-by: Nick Eagles <nickeagles77@gmail.com>
 

 Add a function check_tx_names to change sig_transcripts if ENSEMBL

Co-authored-by: Nick Eagles <nick.eagles@libd.org>
 

 Add check for assayname in assayNames
 

 Fix the code for ENSEMBL and GENCODE annotation

Co-authored-by: Nick Eagles <nick.eagles@libd.org>
 

 Fix unit test and error message for mixed annotation rownames

Co-authored-by: Nick Eagles <nick.eagles@libd.org>
 

 Merge branch 'devel' of github.com:LieberInstitute/qsvaR into devel
 

 Remove ERROR
 

 Fix indentation and remove ERROR with the stop function
 

 Add space and BUG FIXES to the NEWS.md
 

 Add test for when number of rows in 'mod' does not match number of columns in 'rse_tx'
 

 Increment version number to 1.6.0
 

 Rownames discrepancies unit test
 

 Remove expect_true from the unit test
 

 Add check and unit test for Check if all rownames start with "ENST"
 

 Add check if input is a dataframe
 

 Add unit test to test if the input is a dataframe
 

 Fix the logic of the check
 

  Add error message for check if the length of 'common' is greater than 0
 

 Add import tidyverse to the DEqual function
 

 Improve the check if 't' is in the column names of DE
 

 Fix the error message

Co-authored-by: Nick Eagles <nick.eagles@libd.org>
 

 Check if any gene in sig_transcripts is in rownames(rse_tx)

Co-authored-by: Nick Eagles <nick.eagles@libd.org>
 

 Fix the unit tests generating an error
 

 Add a line of code to adjust the rownames in original_results
 

 Improve the unit test where at least one sig_transcript is in covComb_tx_deg rownames
 

 Comment to Check if any gene in sig_transcripts is in rownames(rse_tx)
 

 Change new_transcripts to sig_transcripts
 

 Add sig_transcripts = to the function into the unit test
 

 Update comment
 

 Add select_transcripts to the test
 

 Add check for sig_transcripts in rownames of the rse object
 

 Fix regular expression
 

 Change is_gencode to regular expression to identify if there's .[0-9] trailing
 

 Use all instead of any in getDegTx to check rownames
 

 Add comments to the tests of getDegTx
 

 Use arg_match for type in case user provide invalid type name. Better error message for rse object.
 

 add install from bioc in readme
 

 Deal with rowGeometries setter when removing rowGeometries after all samples have been removed
 

 Bumped version, reoxygenated, belatedly added NEWS.
 

 Save numbers at max precision in JSON lists.
 

 document parallel cores properly
 

 namespace
 

 define and use C-level accessors for SVT leaves

(and clean up code dealing with them)
 

 merge bioc head into dev
 

 Version bump
 

 fixed PUBLICATION tag order when drawn from infolist and absent in settings
 

 Fix #354: Infolist missing COMMENT columns
 

 Merge pull request #1 from MassBank/342

skip executing CCTE examples 

 skip executing CCTE examples
 

 Merge branch 'dev' of https://github.com/tsufz/RMassBank into dev

# Conflicts:
#	man/gatherCCTE.Rd
 

 Add new documentation
 

 Remove non neeed package
 

 Update documentation
 

 Fix missing api_key in example
 

 Move email to general
 

 NOrmalize description and add ORCID
 

 Merge branch 'dev' of https://github.com/tsufz/RMassBank into dev
 

 Merge remote-tracking branch 'origin/350-add_dtxsid_by_api' into dev
 

 Remove artefacts
 

 Add CCTE webaccess functions to retrieve DTXSID, DTXCID, PreferredName and CASRN from US EPA webservices.
 

 Add missing tesseract dependence for magick
 

 Add token to chunk
 

 omg

Merge branch 'dev' of https://github.com/tsufz/RMassBank into dev

# Conflicts:
#	.github/workflows/check-bioc.yml
 

 Fix key

Merge branch 'dev' of https://github.com/tsufz/RMassBank into dev

# Conflicts:
#	.github/workflows/check-bioc.yml
 

 Use the variable
 

 Add specific token.
 

 Merge branch 'dev' of https://github.com/tsufz/RMassBank into dev
 

 Merge branch 'dev' of https://github.com/tsufz/RMassBank into dev
 

 Merge branch 'dev' of https://github.com/tsufz/RMassBank into dev
 

 Add magick as suggestion for vignette building
 

 Move all import calls to central place in zzz.R
 

 writeMgfContent is not exported by MSnbase
 

 Merge branch 'dev' of https://github.com/tsufz/RMassBank into dev
 

 Add glue import to zzz.R
 

 Update namespace
 

 Remove Accession check #338
 

 Fix colon issue
 

 Fix merge conflict issues
 

 Implement tidy import of csv files and fix some issues related.
 

 fixed pipe
 

 Merge branch 'dev' of https://github.com/MassBank/RMassBank into dev
 

 updated docs for accessionBuilder option
 

 Add COPYRIGHT optional column for infolist, addressing #343
 

 Fix #336, export created an additional column, tidy now.
 

 Merge branch 'dev' into ci-bioc-318

# Conflicts:
#	.github/workflows/check-bioc.yml
 

 Print full precision for m/z and intensity, addressing #336
 

 Merge branch 'dev' of https://github.com/MassBank/RMassBank into dev
 

 Merge pull request #332 from tsufz/dev

Add missing License file. 

 Attempt CI with Bioc 3.18 

 Merge pull request #8 from assaron/hsdsdir

Added `type` slot for HSDSFile 

 Merge pull request #6 from AGImkeller/RELEASE_3_19

Release 3 19 

 version bump; updated NEWS; fixed a check error in vignette
 

 changed filter_mode parameter value to avoid check error
 

 other allele mapping
 

 update NEWS
 

 bug fix: use reshape2::melt instead of stats::reshape (#329)

stats::reshape would munge values (typically gene names) 

 Updated NEWS.md and DESCRIPTION

Merged creation of new branch 3.19 on Bioconductor
 

 Speed-up of paramenters estimates (dispersion and nu) (#69)

* Speed-up of the functions `parallelDispersionBisection()` and
`parallelNuBisection()` vias use of `Rfast::rowsums() and
`Rfast::colsums()` respectively

Speed-up of function `logFoldChangeOnClusters()` by using overall
sum for all clusters instead of calculating out-sums each time

Used `torch::torch_mm()` instead of `torch::torch_matmul()` as it
implies less overhead:
it is specialized for 2D tensor multiplications

* Changed default `batchSize` in function `mergeUniformClessClusters`

Improved description notes in vignette

* Minor change in vignette

* Fixed error in vignette

* Fixed issue in `cellsUniformClustering()`:
output cvs about clusters GDI was broken

Now `reorderClusterization()` returns also the clusters' permutation map 

 Now it is possible to use the `torch` library for coex calculations (#67)

* Implemented faster coex evaluations via `torch` library

* Fixed issue with probabilities for negative dispersion genes

* Propagated new torch related parameters upward in the calls' chains

* Fixed issue with torch code: was using too large data type

Dropped unused cores argument from DeaOnCluster()

Aligned tests to new precision

* Added cluster' size to `checkClusterUniformity()` output

* Fixed issue with examples code

* Cleaned-up documentation for more focused man pages

* Added brief document about installing `torch`

Updated the vignette to be more in line with current COTAN usage
  Running uniform clustering functions still takes 20 min,
  so they are still left un-evaluated

Dropped unnecessary lines in `inst/WORDLIST`

* Lowered precision used by `torch` `cpu` devices to 32-bit floats

Fixed some spelling mistakes and non-commond wording 

 version bump in devel
 

 fix bug for gene expression correlation
 

 more refactoring of C code to use new SparseVec typedef
 

 Update for Bioconductor
 

 Fix description
 

 bug fixes
 

 updated update_bam
 

 Merge branch 'taxonomizr' of https://github.com/seanlu96/MetaScope into taxonomizr
 

 removed rBLAST
 

 fixed fasta seqs
 

 staxid
 

 bug fixes
 

 taxid to name fix
 

 Merge branch 'taxonomizr' of https://github.com/seanlu96/MetaScope into taxonomizr
 

 accessiosn_path
 

 bug fixes
 

 Merge branch 'master' of https://github.com/seanlu96/MetaScope
 

 fixed sprintf
 

 Merge branch 'master' of https://github.com/seanlu96/MetaScope

# Conflicts:
#	R/metascope_id.R
 

 add blast_fastas
 

 fix to baselines for get_result_sets
 

 Fixed few reviewer remarks
 

 Fix null pointer exception when reading OMEXML

Closes https://github.com/aoles/RBioFormats/issues/42
 

 Upated version number.

Merge remote-tracking branch 'upstream/devel' into devel

# Conflicts:
#	DESCRIPTION
 

 Added Bioc logo.
 

 version number bump.
 

 added missing package anchors to man pages.
 

 bumped version
 

 Made code more flexible for when annotations lengths are present but not GC
 

 update NEWS
 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 update NEWS
 

 update NEWS
 

 update NEWS
 

 update NEWS
 

 update NEWS
 

 update NEWS
 

 Merge pull request #602 from lgatto/jomain

fix: disable nested parallel processing for chromatograms 

 fix: add ... to `spectra,pSet`
 

 update NEWS
 

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