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[docs] Update NEWS and version
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‎DESCRIPTION‎

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Package: ClustAssess
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Type: Package
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Title: Tools for Assessing Clustering
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Version: 1.0.4
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Authors@R: c(person("Andi", "Munteanu",
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email="am3019@cam.ac.uk", role=c("aut", "cre")), person("Arash", "Shahsavari", email="arash8579@hotmail.com",
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role = c("aut")), person("Rafael", "Kollyfas", role=c("ctb"), email="rk720@cam.ac.uk"), person("Miguel", "Larraz Lopez de Novales", role=c("aut"), email ="ml2088@cam.ac.uk"), person("Liviu", "Ciortuz", role=c("ctb"), email="liviu_ciortuz@yahoo.co.uk"), person("Irina", "Mohorianu",
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email="iim22@cam.ac.uk", role=c("aut")))
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Description: A set of tools for evaluating clustering robustness using
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proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014)
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<doi:10.1038/srep06207>), as well as similarity across methods
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and method stability using element-centric clustering comparison (Gates et
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al. (2019) <doi:10.1038/s41598-019-44892-y>). Additionally, this package
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enables stability-based parameter assessment for graph-based clustering
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pipelines typical in single-cell data analysis.
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License: MIT + file LICENSE
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Encoding: UTF-8
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Additional_repositories: https://blaserlab.r-universe.dev
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biocViews:
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Software,
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SingleCell,
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RNASeq,
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ATACSeq,
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Normalization,
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Preprocessing,
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DimensionReduction,
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Visualization,
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QualityControl,
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Clustering,
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Classification,
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Annotation,
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GeneExpression,
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DifferentialExpression
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Depends:
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R (>= 4.0.0),
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methods,
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stats
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Imports:
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dplyr,
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DT,
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fastcluster,
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foreach,
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glue,
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Gmedian,
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ggnewscale,
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ggplot2,
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ggrastr,
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ggrepel,
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ggtext,
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gprofiler2,
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igraph,
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jsonlite,
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leiden,
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Matrix (>= 1.5.0),
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matrixStats,
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progress,
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stringr,
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paletteer,
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plotly,
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qualpalr,
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RANN,
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reshape2,
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rlang,
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Seurat,
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shiny,
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shinyjs,
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shinyLP,
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shinyWidgets,
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utils,
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uwot,
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vioplot
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RoxygenNote: 7.3.2
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Roxygen: list(markdown = TRUE)
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LinkingTo:
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Rcpp,
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RcppEigen
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Suggests:
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BiocManager,
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colourpicker,
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ComplexHeatmap,
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data.table,
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DelayedMatrixStats,
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devtools,
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doParallel,
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knitr,
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leidenbase,
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monocle3,
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patchwork,
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ragg,
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reticulate,
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rhdf5,
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RhpcBLASctl,
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rmarkdown,
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scales,
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SeuratObject,
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SharedObject,
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styler,
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testthat (>= 3.0.0)
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URL: https://github.com/Core-Bioinformatics/ClustAssess, https://core-bioinformatics.github.io/ClustAssess/
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BugReports: https://github.com/Core-Bioinformatics/ClustAssess/issues
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Config/testthat/edition: 3
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Package: ClustAssess
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Type: Package
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Title: Tools for Assessing Clustering
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Version: 1.0.5
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Authors@R: c(person("Andi", "Munteanu",
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email="am3019@cam.ac.uk", role=c("aut", "cre")), person("Arash", "Shahsavari", email="arash8579@hotmail.com",
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role = c("aut")), person("Rafael", "Kollyfas", role=c("ctb"), email="rk720@cam.ac.uk"), person("Miguel", "Larraz Lopez de Novales", role=c("aut"), email ="ml2088@cam.ac.uk"), person("Liviu", "Ciortuz", role=c("ctb"), email="liviu_ciortuz@yahoo.co.uk"), person("Irina", "Mohorianu",
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email="iim22@cam.ac.uk", role=c("aut")))
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Description: A set of tools for evaluating clustering robustness using
10+
proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014)
11+
<doi:10.1038/srep06207>), as well as similarity across methods
12+
and method stability using element-centric clustering comparison (Gates et
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al. (2019) <doi:10.1038/s41598-019-44892-y>). Additionally, this package
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enables stability-based parameter assessment for graph-based clustering
15+
pipelines typical in single-cell data analysis.
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License: MIT + file LICENSE
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Encoding: UTF-8
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Additional_repositories: https://blaserlab.r-universe.dev
19+
biocViews:
20+
Software,
21+
SingleCell,
22+
RNASeq,
23+
ATACSeq,
24+
Normalization,
25+
Preprocessing,
26+
DimensionReduction,
27+
Visualization,
28+
QualityControl,
29+
Clustering,
30+
Classification,
31+
Annotation,
32+
GeneExpression,
33+
DifferentialExpression
34+
Depends:
35+
R (>= 4.0.0),
36+
methods,
37+
stats
38+
Imports:
39+
dplyr,
40+
DT,
41+
fastcluster,
42+
foreach,
43+
glue,
44+
Gmedian,
45+
ggnewscale,
46+
ggplot2,
47+
ggrastr,
48+
ggrepel,
49+
ggtext,
50+
gprofiler2,
51+
igraph,
52+
jsonlite,
53+
leiden,
54+
Matrix (>= 1.5.0),
55+
matrixStats,
56+
progress,
57+
stringr,
58+
paletteer,
59+
plotly,
60+
qualpalr,
61+
RANN,
62+
reshape2,
63+
rlang,
64+
Seurat,
65+
shiny,
66+
shinyjs,
67+
shinyLP,
68+
shinyWidgets,
69+
utils,
70+
uwot,
71+
vioplot
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RoxygenNote: 7.3.2
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Roxygen: list(markdown = TRUE)
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LinkingTo:
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Rcpp,
76+
RcppEigen
77+
Suggests:
78+
BiocManager,
79+
colourpicker,
80+
ComplexHeatmap,
81+
data.table,
82+
DelayedMatrixStats,
83+
devtools,
84+
doParallel,
85+
knitr,
86+
leidenbase,
87+
monocle3,
88+
patchwork,
89+
ragg,
90+
reticulate,
91+
rhdf5,
92+
RhpcBLASctl,
93+
rmarkdown,
94+
scales,
95+
SeuratObject,
96+
SharedObject,
97+
styler,
98+
testthat (>= 3.0.0)
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URL: https://github.com/Core-Bioinformatics/ClustAssess, https://core-bioinformatics.github.io/ClustAssess/
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BugReports: https://github.com/Core-Bioinformatics/ClustAssess/issues
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Config/testthat/edition: 3

‎NEWS.md‎

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# Unreleased
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### Updates
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- Add barplot with Cell count or percentage of metadata in the Shiny context.
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- Add option to combine (split) metadata and dynamically create a new metadata column in the Shiny context.
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- Add option to calculate the percentage of cells expressing gene above a threshold in the summary table from the Shiny Violin section.
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### Fixes
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- Fix the case in `write_object` when the gene variance filtering leaves the chunk with one or zero genes.
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- Stop allowing the user to calculate the ECC or perform the merging to a list with less than two partitions by raising an exception.
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## version 1.1.0
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---
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### Updates
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- Add barplot with Cell count or percentage of metadata in the Shiny context.
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- Add option to combine (split) metadata and dynamically create a new metadata column in the Shiny context.
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- Add option to calculate the percentage of cells expressing gene above a threshold in the summary table from the Shiny Violin section.
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- Add hierarchical plot that shows the relationship between partitions with different number of clusters.
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### Fixes
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- Fix the case in `write_object` when the gene variance filtering leaves the chunk with one or zero genes.
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- Stop allowing the user to calculate the ECC or perform the merging to a list with less than two partitions by raising an exception.
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- Sort the k values numerically in the `merge_resolutions` function.

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