NEWS.md
In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

pRoloc 1.45

pRolocmarkers() has a new version argument, to allow for new markers versions to be added.
14 new marker sets have been added to pRolocmarkers() under version = 2 (new default).
Documentation for pRolocmarkers() has been updated to include a description of version = 2 markers.

Import 'mclust::estep*()'.

New devel version

pRoloc 1.43

Fix/update dunkley2006param object.

Fix syntax in man pages.

New devel version

pRoloc 1.39

Update transfer learning vignette to use hpar 1.41.

New devel version (Bioc 3.17)

pRoloc 1.37

Fix bug in PerTubro classifiction function (see #146 and #147), contributed by mgerault.

pRoloc 1.33

pRoloc 1.31

Fix failing unit test, by setting RNGseed in SerialParam() (fix by ococrook, see #142).

New devel version (Bioc 3.14)

lopims() function moved to lgatto/lopims package on GitHub

Update dunkley2006params, andy2011params and MartInterfaces objects

Suggest magick (needed to build vignette)

New devel version (Bioc 3.13)

pRoloc 1.29

New devel version (Bioc 3.12)

Removed duplicate colour in getStockCol and updated the colour palette

pRoloc 1.28

New release version (Bioc 3.11)

pRoloc 1.27

Depend on MLInterfaces 1.67.10

import stats4::plot <2020-03-26 Thu>

Import missing mclust::mclustBIC

Remove exprsToRatio man page (function in MSnbase and is deprecated)

Fix errors related to R-devel

Merged plotting payes PR

Version bump for Bioc 3.11 (devel)

pRoloc 1.25

New spatial2D function <2019-09-24 Tue>

Fix new biomart attribute <2019-08-09 Fri>
Bug fix: pass fcol to helper function (see https://support.bioconductor.org/p/123614/) <2019-08-09 Fri>

Always use mvtnorm::dmvnorm <2019-06-21 Fri>

Version bump for Bioc 3.10 (devel)

pRoloc 1.24

Version bump for Bioc 3.9 (release)

pRoloc 1.23

Remove plain NEWS now that R supports NEWS.md

Link to TAGM F1000 workflow <2019-04-11 Thu>
Add ref to TAGM F1000 in CITATION and README <2019-04-11 Thu>
Update biomart interface data and AnnotationParams-related code <2019-04-12 Fri>

Add mcmc helper functions.
New logPosteriors accessor for MAPParams object.
New plotConsProfiles function, contributed by Tom Smith (see PR #131).
Update TAGM vignette, refering to workflow <2019-03-14 Thu>

Add note about missing data in QSep man <2018-10-31 Wed>
Add mcmc-helper documentation <2018-11-04 Sun>
Fixing numerical instability in Cholesky decomposition (see #124) <2018-11-30 Fri>
Add option to display or not display grid in plot2D <2018-12-12 Wed>
mrkHClust now uses mrkConsProfiles and returns the hclust object - see issue #130 for details and background <2018-12-19 Wed>

New version for Bioc 3.9 devel

pRoloc 1.22

New version for Bioc 3.8 release

pRoloc 1.21

Fix type in vignette header <2018-09-18 Tue>
Fix bug in plot method for ThetaRegRes object <2018-09-24 Mon>

Add an fcol argument to plotDist to plot and colour all profiles <2018-08-09 Thu>

Use BiocManager in vignette
Fix bug in plot2D: pass ... to hexbin <2018-08-02 Thu>

Use BiocManager in installation instructions

Added new section in Bayesian spatial proteomics vignette detailing mcmc output processing <2018-07-07 Sat>

Fix bugs in tagmMcmcPredict, where fcol was ignored <2018-06-05 Tue>
Order vignettes by prefixing the files with numbers <2018-06-05 Tue>

New TAGM-MCMC generative model, contributed by Oliver Crook <2018-05-18 Fri>

Version bump for BiocStyle update: Vignette needed to be rebuilt to have bug fixed in BiocStyle footnote rendering.

Fix bug in higlightOnPlot with missing fcol (see #105) <2018-05-03 Thu>
New TAGM-MAP generative model, contributed by Oliver Crook <2018-05-18 Fri>
New plotEllipse function to visualise and assess TAGM models <2018-05-18 Fri>

pRoloc 1.20

New Bioconductor release 3.7

pRoloc 1.19

Fix regression bug in knntl function <2018-04-12 Thu>

Use dplyr::left_join without attaching dplyr to avoid collision between Biobase::exprs and dplyr::exprs <2018-04-04 Wed>.
Typo in warning to install rgl <2018-03-27 Tue>

Fix bug in QSep that prevented to set non-default fcol <2018-01-29 Mon>

Fix bug in private dimred and set appropriate number of colnames <2017-11-07 Tue>
New nipals method in dimensionality reduction for plot2D (closes issue #103) <2018-01-16 Tue>

Bioconductor devel 3.7

pRoloc 1.18

Bioconductor release 3.6

pRoloc 1.17

Filtering for unique features when running plot2D with t-SNE method <2017-10-15 Sun>

Added new (private) dimred function that computes dimensionality reduction <2017-06-05 Mon>
Add F1000research workflow to citations <2017-06-22 Thu>
Classification functions now return the classification score matrix for all classes as a single column in fData, rather that each class as its own fData column. <2017-09-01 Fri>

Convert vignettes to Rmd with html output <2017-05-25 Thu>
Import, rather than suggest Rtsne <2017-05-25 Thu>

phenoDisco speed improvements and added support for t-SNE <2017-05-19 Fri>

Support Rtsne's new pca_center and pca_scale arguments <2017-05-02 Tue>

Version bump for Bioc devel 3.6

MSnbase 1.16

Version bump for Bioc release 3.5

MSnbase 1.15

update biomart attribute names to relect changes <2017-04-20 Thu>

New mrkConsProfiles function to calculate average/consensus marker profiles <2017-04-11 Tue>

Fix warnings and notes <2017-02-25 Sat>
Add section about dimensionality methods reduction and t-SNE in the tutorial <2017-03-07 Tue>
Fix error due to new uniprot attribute names <2017-04-06 Thu>

fix (unexported) remap function - see issue #92 <2016-12-15 Thu>
plot2Ds now only adds segments when the featureNames are identical <2017-01-11 Wed>
Import (rather than Suggest) hexbin <2017-01-18 Wed>
Increase margin in QSep plotting (contributed by S. Gibb) <2017-02-07 Tue>

Update plotDist to use sampleNames() to label x axis ticks and getUnknowncol() as default pcol (see issue #91) <2016-11-08 Tue>
xlab and ylab are args in plotDist <2016-12-04 Sun>

Update human markers - see pRolocdata's issue 21 https://github.com/lgatto/pRolocdata/issues/21 <2016-11-08 Tue>

Fix bug in plot2D to ignore fcol when using hexbin method <2016-11-04 Fri>

Fix Arabidopsis parameters for biomaRt questions: 'TAIR locus ID' is now 'Stable gene ID'. Changed in several manual files and dunkley2006params. <2016-11-02 Wed>

new plot3D function <2016-10-27 Thu>
update CITATION <2016-10-27 Thu>
use predict:::predict.plsa, as it is not exported anymore <2016-11-01 Tue>

MSnbase 1.13

removing visualTest from suggest, as plotting tests currently disabled (see https://github.com/MangoTheCat/visualTest/issues/19 for details) <2016-10-07 Fri>

Fix bug in plot,QSep with NAs <2016-09-09 Fri>
Adapt tl vignette to new hpar <2016-09-15 Thu>

Pass ... in levelPlot,QSep <2016-09-06 Tue>
Various improvements to the tutorial vignette <2016-09-07 Wed>
Fix bug in QSep to honour fcol <2016-09-09 Fri>

Added plot3D, equivalent to plot2D, but using rgl in 3 dimensions <2016-09-03 Sat>
Parametrise logging in knntlOptimisation to reduce object size <2016-09-06 Tue>
New mrkHClust function to plot a dendrogram of subcellular markers <2016-09-06 Tue>

Remove verbose argument from getMarkerClasses function <2016-08-23 Tue>
plot2D has new addLegend argument <2016-08-23 Tue>
addLegend default position is now bottomleft (requested by Lisa) <2016-08-23 Tue>
new hexbin plot2D method <2016-08-28 Sun>

Add a norm agument to QSep's plotting functions to visualise normalised and raw distances <2016-08-22 Mon>
New zeroInBinMSnSet function to visualise rowSums <2016-08-23 Tue>

Send biomart queries in getGOFromFeatues in chunks - see issue #85 for details <2016-08-20 Sat>

new QSep infrastructure to assess spatial resolution <2016-08-17 Wed>
Use %age of total variance in plot2D's scree plot <2016-08-17 Wed>
fixed bug in combineThetaRegRes <2016-08-19 Fri>

fDataToUnknown accepts from = NA <2016-08-10 Wed>

Added an lda method to plot2D <2016-08-08 Mon>

Fixed bug in addGoAnnotations <2016-07-29 Fri>

Fixed bug in show method for ThetaRegRes <2016-06-08 Wed>
Profiled knntl code so it's now much faster. Added more unit tests for knntl <2016-06-10 Fri>
Fixed bug in plotDist x-axis labelling <2016-06-14 Tue>

Updated mouse pRolocmarkers <2016-06-02 Thu>

Fix bug in mirrorX/Y highlightOnPlot - see problem 1 in issue #79 <2016-05-31 Tue>

Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if R_CHECK_TIMINGS is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more. d.tenenbaum

Added keepNA argument to goTermToId so that if a GO term becomes obsolete and you cannot replace it with the ID name, you have the option to either replace it with a NA (previous and current default option) or now with keepNA = FALSE the term name will be replaced with the id name <2016-05-25 Wed>
Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included. d.tenenbaum

Version bump for new Bioc devel

MSnbase 1.12

Version bump for Bioc release version 3.3

MSnbase 1.11

New gomarkers functionality for adding annotation information to spatial proteomics data and accompanying new vignette <2016-04-18 Mon>
Added unit tests <2016-04-20 Wed> <2016-04-21 Thu>
Moved makeNaData[2] and whichNA to MSnbase <2016-04-21 Thu>
Renamed addGoMarkers and orderGoMarkers to addGoAnnotations and orderGoAnnotations and all associated documentation. Vignette also renamed to pRoloc-goannotations <2016-04-21 Thu>

fix bug in knntlOptimisation to allow passing of th matrix with 1 column <2016-04-08 Fri>

fix bug in getParams method = 'max' <2016-04-07 Thu>

Update plotDist signature to support different types and pch <2016-04-05 Tue>

Update dunkley2006params <2016-04-01 Fri>

Update dunkley2006params <2016-03-30 Wed>

Selective imports <2016-03-20 Sun>

Update dunkley2006params <2016-04-01 Fri>

Update dunkley2006params <2016-03-30 Wed>

Selective imports <2016-03-20 Sun>

Update package startup msg <2016-03-11 Fri>

Clarify that score during optim are not a reflection of final assignment accuracy <2016-03-01 Tue>

fix build error due to doi/url confusion <2016-03-01 Tue>

new method argument added to knntlOptimisation that allows optimisation of class weights as per Wu and Dietterich's original k-NN TL method <2016-02-19 Fri>
seed argument added to knntlOptimisation for reproducibility <2016-02-22 Mon>
New section in tl vignette describing preparation of auxiliary PPI data <2016-02-29 Mon>

the colour and pch setters now invisibly return the old values <2016-02-17 Wed>

added error message when sampleNames differ between datasets in an MSnSetList when using remap function <2016-02-11 Thu>

Update colours man page to document change in default colour palette <2016-02-08 Mon>

Lisa's colour palette is now default. Old colours can be accessed and set with get/setOldcol <2016-02-04 Thu>

New Lisa cols and changed default unknown col <2016-02-03 Wed>
mrkVecToMat has been updated so that the column order reflects the factor levels of fcol, rather than calling unique on fcol. This change means that the order of the classes in fcol are now consistent between plot2D and new visualisation apps that rely on mrkVecToMat. <2016-02-03 Wed>

Various non-visible changes. <2016-01-19 Tue>

new classWeights function <2015-12-26 Sat>

highlightOnPlot support labels = TRUE to use featureNames as labels <2015-12-21 Mon>
selective ggplot2 import <2015-12-21 Mon>
highlightOnPlot also support a vector of feature names in addition to an instance of class FeaturesOfInterest <2015-12-21 Mon>

plot2D: Mirror PCs even when not plotting, addressing issue #68 <2015-12-18 Fri>

Update dunkley2006params to use plant_mart_30 <2015-12-16 Wed>
API change in plot2D: to plot data as is, i.e. without any transformation, method can be set to "none" (as opposed to passing pre-computed values to method as in previous versions). If object is an MSnSet, the untransformed values in the assay data will be plotted. If object is a matrix with coordinates, then a matching MSnSet must be passed to methargs. <2015-12-16 Wed>

Internally using MartInterface to query individual mart servers to bypass the biomart.org downtime <2015-12-09 Wed>

New orgQuants function and update to getPredictions <2015-10-13 Tue>
Deprecate minClassScore replaced by getPredictions <2015-10-19 Mon>
Add pRolocVisMethods and check for new apps in pRolocGUI <2015-10-19 Mon>
new fDataToUnknown function <2015-10-23 Fri>
New section in vignette describing readMSnSet2 <2015-11-30 Mon>

Bioc devel version 3.3

MSnbase 1.10

Bioc release version 3.2

MSnbase 1.9

New SpatProtVis visualisation class <2015-08-13 Thu>
add link to explanation of supportive/uncertain reliability scores in tl vignette <2015-09-02 Wed>

Update REAMDE with TL ref
Update refs in lopims documentation <2015-07-30 Thu>

update doc <2015-07-15 Wed>

Add reference to TL paper and link to lpSVM code <2015-07-06 Mon>
highlightOnPlot throws a warning and invisibly returns NULL instead of an error when no features are in the object <2015-07-08 Wed>
highlightOnPlot has a new labels argument <2015-07-10 Fri>

Clarify error when no annotation params are provided <2015-05-11 Mon>
support for matrix-encoded markers <2015-05-19 Tue>
New default in addLegend: bty = "n" <2015-05-20 Wed>
getMarkers now supports matrix markers <2015-05-20 Wed>
getMarkerClasses now supports matrix markers <2015-05-20 Wed>
markerMSnSet and unknownMSnSet now support matrix markers <2015-05-20 Wed>
sampleMSnSet now supports matrix markers <2015-05-23 Sat>
updated yeast markers and added uniprot ids <2015-05-27 Wed>
plot2D support a pre-calculated dim-reduced data matrix as method parameter to avoid recalculation <2015-05-27 Wed>

Lisa's colour palette <2015-05-08 Fri>

new plot2Ds function to overlay two data sets on the same PCA plot [2015-04-17 Fri]
regenerate biomart data used by setAnnotationParams [2015-04-24 Fri]
new setStockcolGui function to set the default colours manually via a simple interface [2015-04-29 Wed]
new move2Ds function to produce an transition movie between two MSnSets [2015-04-29 Wed]
functions to convert GO ids to/from terms. See ?goTermToId for details <2015-05-08 Fri>

new devel version for Bioc 3.2

MSnbase 1.7

use donttest instead of dontrun [2015-04-09 Thu]

don't run knntl example to reduce checking time and timeout on Windows [2015-04-08 Wed]

fix splitTh, closes issue #49 [2015-04-06 Mon]

Change in vignette to work on zin1: using 12 random th rows. See issue #49 for details. Fixed in version 1.7.11. [2015-04-03 Fri]

updated tl vignette [2015-04-02 Thu]
depending on latest (1.5.8) pRolocdata [2015-04-02 Thu]

updating tl vig [2015-04-02 Thu]
update getParams documentation [2015-04-02 Thu]

renaming theta.scores to knntl.scores [2015-03-24 Tue]

added the theta inductive transfer infrastructure [2015-02-05 Thu]
theta vignette stub [2015-02-06 Fri]
rename getClasses to getMarkerClasses [2015-02-06 Fri]
added the infrastructure to create GO MSnSet [2015-02-07 Sat]
Fixed ml vignette [2015-02-16 Mon]
new filterZeroRows function [2015-03-10 Tue]
hpa data section [2015-03-10 Tue]
theta sections [2015-03-10 Tue]
deprecate getRegulari[z|s]edParams [2015-03-11 Wed]

Fix vignettes: run bibtex and pdflatex twice and typo [2015-02-03 Tue]

Use default Sweave call to build vignette [2015-01-24 Sat]

use Biocstyle [2015-01-23 Fri]
replace library/require by requireNamespace [2015-01-23 Fri]

added t-SNE method to plot2D [2015-01-14 Wed]
Updated NAMESPACE imports [2015-01-14 Wed]

updated vignettes with markers.orig [2014-10-30 Thu]
updated ml tests [2014-10-30 Thu]

new devel version, Bioc 3.1

MSnbase 1.6

new stable version, Bioc 3.0

MSnbase 1.5

added Video tag in DESCRIPTION [2014-10-07 Tue]

HUPO 2014 poster [2014-01-02 Thu]

fix 'replacing previous import by MLInterfaces::plot when loading pRoloc' warning by using specific importFrom [2014-09-27 Sat]

new pRolocGUI section [2014-08-15 Fri]
new foi section [2014-08-16 Sat]

svmOpt sigma defaults changed from 10^(-2:3) to 10^(-3:2) [2014-08-15 Fri]
in xxxOptimisation, the best parameter(s) for the validation classification runs are now chosen at random instead of using the first best param (see change in pRoloc:::getBestParam that got a sample argument defaulted to TRUE) [2014-08-15 Fri]
When calculating macroF1 scores (xval and validation), NAs are set to 0 (via MLInterfaces:::.macroF1(..., naAs0 = TRUE)). The macro F1 will not be NA (when mean of F1s is calculated) but lowered. This avoids having an NA macro F1 when 1 (or more) classe(s) end(s) up with NA (also set to 0) precision(s) or recall(s) [2014-08-15 Fri]

add title to plotDist figures [2014-08-13 Wed]

none

support mirrorX/mirrorY in highlightOnPlot [2014-07-22 Tue]

Remove plot2D outliers param [2014-07-10 Thu]
fix subsetAsDataFrame for keepColNames and write unit test [2014-07-11 Fri]

alias lopims4 function [2014-07-01 Tue]

Export single steps of lopims [2014-06-23 Mon]
Rephrase classifier parameter optimisation proceudres [2014-06-23 Mon]

nndistx_matrix function added to allow use of query matrix when calculating knn distances [2014-06-18 Wed]
nndist[x]_[matrix|msnset] are now available using the experted nndist method [2014-06-18 Wed]
markerSet and unknownSet renamed to markerMSnSet and unknownMSnSet [2014-06-19 Thu]
functions sampleMSnSet and testMSnSet added [2014-06-19 Thu]
fix keepColNames in pRoloc:::subsetAsDataFrame - fcol was always renamed to "markers" [2014-06-19 Thu]

add recommended biocView [2014-06-05 Thu]

addMarkers has a new mcol argument to set the markers feature variable label [2014-05-29 Thu]

replaced MSVBAR::rmultnorm with mvtnorm::rmvnorm since the former has been removed from CRAN and don't import [2014-05-21 Wed]
Bug tracking [2014-05-26 Mon]

testMarkers gets an error argument [2014-05-14 Wed]
plotDist now has a ylim argument [2014-05-21 Wed]

import all MLInterfaces [2014-04-30 Wed]
new param optim secion in ml vignette [2014-05-05 Mon]
various ml typos and pRolocmakers man update [2014-05-06 Tue]

In plotDist, ... is now passed to matlines instead of plot and has a new lty parameter [2014-04-17 Thu]
new highlightOnPlot function, using the new features of interest infrastructure [2014-04-29 Tue]

new dunkley2006 pdunit object created with mclust 4.3 [2014-04-08 Tue]
addMarker also accepts fcol and addMarkers unit test [2014-04-14 Mon]

Bioc devel 3.0

MSnbase 1.4

Bioc release 2.14

MSnbase 1.3

fixed error introduced with mclust 4.3 (that now returns the data in the Mclust output - see comment in pRoloc:::gmmOutliers for details) [2014-04-07 Mon]

getPredictions can take class-specific scores [2014-04-04 Fri]

fixed newly introduced bug (see 1.3.16) in pRoloc:::subsetAsDataFrame - thank you unit tests for saving me, again [2014-03-26 Wed]

pRoloc:::subsetAsDataFrame now preserved original sample/column names [2014-03-24 Mon]
fixed wrong message when using col and pch in plot2D [2014-03-25 Tue]

updated pRolocmarkers("mmus") [2014-03-21 Fri]
moved extdata/*csv to pRolocdata [2014-03-23 Sun]
using *csv from pRolocdata [2014-03-23 Sun]

deleted tab character [2014-03-15 Sat]
added support for GMM parametrisation to phenoDisco [2014-03-17 Mon]
message instead of warning when using colour and pch [2014-03-21 Fri]
remove 1 duplicated mouse marker [2014-03-21 Fri]

fixed a bug in addLegend [2014-03-14 Fri]
updated testing to testthat 0.8 [2014-03-14 Fri]
Fixing several warnings about symnbols being replaced upon pRoloc loading and note about usage of ::: [2014-03-15 Sat]

added phenoDisco2 for testing, allows choice of GMM parameters [2014-02-26 Wed]
removed duplicated fly markers [2014-02-28 Fri]
updated affiliations in vignettes [2014-03-10 Mon]

modify to new biocViews to DESCRIPTION file by s.arora [2014-03-04]

new phenoDisco ndims argument to use more than two two principal components as input for discovery analysis [2014-01-03 Mon]
fixed and updated phenoDisco logging [2014-02-03 Mon]
added support for parallel phenoDisco execution. See BPPARAM argument [2014-02-03 Mon]
fixed issues with using PD and ndims [2014-02-10 Mon]
fixed call to anyUnknown in PD code [2014-02-10 Mon]
checking if duplicated markers in addMarkers [2014-02-14 Fri]

bump to force rebuild for new Rcpp

Removed trailing space in mmus nucleus markers [2014-01-21 Tue]
using filterNA to remove features with missing values in plot2D [2014-01-21 Tue]
fixed plot2D/addLegend [2014-01-23 Thu]

fixed addLegend to use correct colours (order) [2014-01-20 Mon]
fix typo in addMarkers man [2014-01-20 Mon]
re-arranged stockpch so that interleave full and empty plotting character [2014-01-20 Mon]
Removed last stockcol (tomato), too cose to "#FF7F00" [2014-01-20 Mon]

updated human markers: keep new pd.markers phenotypes, validated by Lisa and remove singletons [2014-01-14 Tue]
first stockpch is noe 19 [2014-01-16 Thu]
plot2D(.., pch) now taken into account for labelled data [2014-01-16 Thu]
removed alpha plot2D argument [2014-01-17 Fri]
updated plot2D and addLegend function with support for more organelle groups than colours. The previous versions are available as plot2D_v1 and addLegend_v1. [2014-01-17 Fri]

pRoloc citation [2014-01-12 Sun]

new unknownSet function [2013-12-11 Wed]
updated vignettes to account for tan2009r1 changes [2013-12-16 Mon]

update citation in phenoDisco.Rd [2013-11-22 Fri]
typos in vignettes [2013-11-25 Mon]

new markers [2013-11-06 Wed]
markers in vinette [2013-11-15 Fri]
mouse markers [2013-11-18 Mon]

using combineFeatures(..., na.rm=TRUE) in lopims pipeine [2013-10-22 Tue]
corrected spelling errors in phenoDisco doc [2013-10-29 Tue]

next devel version fot Bioc 2.14

MSnbase 1.1

semi-sup and sup comparison sections in ml vig [2013-10-09 Wed]

getMarkers has names arg [2013-10-01 Tue]

new outliers arg to plot2D [2013-09-23 Mon]
cite addMarkers in vignette [2013-09-26 Thu]
add code chunk in poster vig [2013-09-26 Thu]

added biocViews [2013-09-19 Thu]
added knitr vig engine in ml [2013-09-19 Thu]
import dependencies [2013-09-20 Fri]

building ml vignette in Makefile [2013-09-11 Wed]

new private anyUnknown function, used in phenoDisco, to check for the presence of unlabelled ('unknown') data [2013-08-27 Tue]
added a note in vignette about "unknown" convention to define protein with unknown localisation [2013-08-28 Wed]
Added HUPO 2011 poster [2013-09-09 Mon]

fixed Author[s]@R [2013-05-16 Thu]
na.rm=TRUE in f1Count [2013-05-19 Sun]
added CITATION file [2013-06-07 Fri]
new testMarkers function [2013-06-29 Sat]
error message in getBestParams suggests to use testMarkers [2013-06-29 Sat]
nndist methods (see issue #23) [2013-07-01 Mon]
remove unnecessary as.matrix in plot2D's cmdscale [2013-07-19 Fri]
added plot2D(..., method = "MDS") example [2013-07-19 Fri]
changed 'euclidian' to 'euclidean' in nndist_matrix [2013-07-26 Fri]
fixed row ordering in phenoDisco, input and output rownames are now the same [2013-08-13 Tue]
Using filterNA in phenoDisco [2013-08-13 Tue]

Update README.md to reflect availability in stable release and biocLite installation [2013-04-07 Sun]
new MSe pipeline [2013-04-07 Sun]
perTurbo using Rcpp [2013-04-16 Tue]
initial clustering infrastructure (not exported) [2013-04-17 Wed]
new markerSet function [2013-04-24 Wed]
plsaOptim's ncomp is now 2:6 [2013-04-27 Sat]
added forword to vignette [2013-04-29 Mon]
default k is now seq(3, 15, 2) in knnOptim [2013-05-09 Thu]

Bioc 2.13 devel version bump

MSnbase 1.0

Bioc 2.12 stable version bump

MSnbase 0.99

illustrating class.weights in the vignette [2013-03-24 Sun]

new addMarkers function [2013-03-22 Fri]

Fixing issues in vignette [2013-03-22 Fri]

Added scale in tutorial [2013-03-02 Sat]
implemented viction [2013-03-09 Sat]
New vignette section on phenoDisco follow up classification [2013-03-19 Tue]
Using knitr engine [2013-03-19 Tue]

depending on MSnbase ]= 1.7.23 as makeNaData needs MSnbase:::nologging [2013-02-27 Wed]
updated phenoDisco parameters, added error messages when an insufficient number of markers per class and/or number of classes are used and updated phenoDisco help file [2012-02-28 Thu]
added first belief diffscores function [2013-03-01 Fri]

plot2D has gained a plot argument [2013-02-19 Tue]
new f1Count method [2013-02-20 Wed]
new makeNaData function [2013-02-20 Wed]
new makeNaData2 function [2013-02-21 Thu]
new whichNAfunction [2013-02-20 Wed]
updated tutorial vignette [2013-02-20 Wed]
Now passing ... to predictor functions in xxxClassification (reported by Marianne Sandin) [2013-02-26 Tue]

setUnknowncol(NULL) and friedns reset to default values [2013-02-19 Tue]

new default col/pch setters [2013-02-16 Sat]

Updates to phenoDisco: verbose param, fixed error in example, adding params to processingInfo [2013-02-11 Mon]
Unexported getOtherParams method [2013-02-12 Tue]
adding export param documentation [2013-02-12 Tue]

Integration of the perTurbo algorithms, contributed by Thomas Burger and Samuel Wieczorek [2013-01-18 Fri]
summariseMatList now has na.rm = TRUE by default [2013-01-19 Sat]
PerTurbo's inv/reg now as other hyperparams [2013-02-11 Mon]

knitr 1.0 compatibility [2013-01-15 Tue]
Updated phenoDisco documentation and README [2013-01-10 Thu]

removed updateClass man [2013-01-03 Thu]
removed old Rd files [2013-01-03 Thu]
Deprecating Regularisation and Prediction function [2013-01-03 Thu]
Updated new names in test_ml.R [2013-01-04 Fri]

more reg data into GenRegRes objects
cmMatrices (knn) [2012-11-15 Thu] (other) [2012-11-30 Fri]
testPartitions (knn) [2012-11-17 Sat] (other) [2012-11-30 Fri]
new minMarkers function [2012-11-16 Fri]
renamed updateClass to minClassScore [2012-11-16 Fri]
renamed xxxRegularisation to xxxOptimisation [2012-11-30 Fri]
renamed xxxPrediction to xxxClassification [2012-11-30 Fri]
renamed getRegularisedParams to getParams [2012-11-30 Fri]
moved exprsToRatios to MSnbase [2012-12-05 Wed]
updated phenoDisco help file [2012-12-07 Fri]
updated phenoDisco code to cope with identical protein profiles [2012-12-07 Fri]

Adding README file describing Rd generation and suggesting roxygen2 [2012-11-14 Wed]
Added scol=NULL to ignore completely [2012-11-14 Wed]

pdres in extdata - updated vignette [2012-11-14 Wed]
udpated pd's GS/times default [2012-11-14 Wed]

fixed MLearn("formula", "MSnSet", "clusteringSchema", "missing") - interface was wrong [2012-11-10 Sat]
vignette updates [2012-11-10 Sat] [2012-11-11 Sun]
nicer knn score names when scores = "all" [2012-11-11 Sun]

updated exprsToRatio when ncol(object) is 2 [2012-11-05 Mon]
typos in vignette [2012-11-09 Fri] [2012-11-10 Sat]
new MLearn method for signature c("formula", "MSnSet", "clusteringSchema", "missing") [2012-11-09 Fri]
Several vignette udpates [2012-11-10 Sat]

Submission to Bioc [2012-11-04 Sun]

lgatto/pRoloc documentation built on Oct. 23, 2024, 12:51 a.m.

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lgatto/pRoloc A unifying bioinformatics framework for spatial proteomics

NEWS.md In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

pRoloc 1.45

Changes in version 1.45.2

Changes in version 1.45.1

Changes in version 1.45.0

pRoloc 1.43

Changes in version 1.43.2

Changes in version 1.43.1

Changes in version 1.43.0

pRoloc 1.39

Changes in version 1.39.1

Changes in version 1.39.0

pRoloc 1.37

Changes in version 1.37.1

pRoloc 1.33

pRoloc 1.31

Changes in version 1.31.1

Changes in version 1.31.0

Changes in version 1.31.3

Changes in version 1.31.2

Changes in version 1.31.1

Changes in version 1.31.0

pRoloc 1.29

Changes in version 1.29.0

Changes in version 1.29.1

pRoloc 1.28

Changes in version 1.28.0

pRoloc 1.27

Changes in version 1.27.6

Changes in version 1.27.5

Changes in version 1.27.4

Changes in version 1.27.3

Changes in version 1.27.2

Changes in version 1.27.1

Changes in version 1.27.0

pRoloc 1.25

Changes in version 1.25.3

Changes in version 1.25.2

Changes in version 1.25.1

Changes in version 1.25.0

pRoloc 1.24

Changes in version 1.24.0

pRoloc 1.23

Changes in version 1.23.4

Changes in version 1.23.3

Changes in version 1.23.2

Changes in version 1.23.1

Changes in version 1.23.0

pRoloc 1.22

Changes in version 1.22.0

pRoloc 1.21

Changes in version 1.21.9

Changes in version 1.21.8

Changes in version 1.21.7

Changes in version 1.21.6

Changes in version 1.21.5

Changes in version 1.21.4

Changes in version 1.21.3

Changes in version 1.21.2

Changes in version 1.21.1

pRoloc 1.20

Changes in version 1.20.0

pRoloc 1.19

Changes in version 1.19.4

Changes in version 1.19.3

Changes in version 1.19.2

Changes in version 1.19.1

Changes in version 1.19.0

pRoloc 1.18

Changes in version 1.18.0

pRoloc 1.17

Changes in version 1.17.5

Changes in version 1.17.4

Changes in version 1.17.3

Changes in version 1.17.2

Changes in version 1.17.1

Changes in version 1.17.0

MSnbase 1.16

Changes in version 1.16.0

lgatto/pRoloc
A unifying bioinformatics framework for spatial proteomics

NEWS.md
In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics