Commit bb091560 authored by Christian Arnold's avatar Christian Arnold
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Small improvements

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Package: GRaNIE
Title: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
Version: 0.14.0
Version: 0.14.1
Encoding: UTF-8
Authors@R: c(person("Christian", "Arnold", email =
"christian.arnold@embl.de", role = c("cre","aut")),
......
## GRaNIE 0.9 - 0.14 (2021-12-13)
# GRaNIE 0.9-0.14 (2021-12-13)
### Major changes
## Major changes
- major overhaul and continuous work on peak-gene QC plots
- the *filterData* functions has now more filter parameters, such as filtering for CV. Also, all filters uniformly have a *min* and *max* filter.
......@@ -8,63 +8,63 @@
- handling of edge cases and rare events in various functions
- packages have been renamed to *GRaNIE* as basename (before: *GRN*)
### Bug fixes
## Bug fixes
- various minor bug fixes
### Minor changes
## Minor changes
- changed the object structure slightly and moved some gene and peak annotation data (such as mean, CV) to the appropriate annotation slot
## GRaNIE 0.8 (2021-05-07)
# GRaNIE 0.8 (2021-05-07)
### Major changes
## Major changes
- improved PCA plotting, PCA plots are now produced for both raw and normalized data
- new filters for the function *filterGRaNIEAndConnectGenes* (*peak_gene.maxDistance*) as well as more flexibility how to adjust the peak-gene raw p-values for multiple testing (including the possibility to use IHW - experimental)
- new function *plotDiagnosticPlots_TFPeaks* for plotting (this function was previously called only internally, but is now properly exported), in analogy to *plotDiagnosticPlots_peakGene*
### Bug fixes
## Bug fixes
- various minor bug fixes (PCA plotting, compatibility when providing pre-normalized data)
### Minor changes
## Minor changes
- changed the object structure slightly and cleaned the config slot, for example
- some functions have been added / renamed to make the workflow more clear and streamlined, see Vignette for details
- some default parameters changed
## GRaNIE 0.7 (2021-03-12)
# GRaNIE 0.7 (2021-03-12)
### Major changes
## Major changes
- improved PCA plotting, also works for pre-normalized counts now when provided as input originally
- more flexibility for data normalization
- homogenized wordings, function calls and workflow clarity, removed unnecessary warnings when plotting peak-gene diagnostic plots, added more R help documentation
- added IHW (Independent Hypothesis Weighting) as a multiple testing procedure for peak-gene p-values in addition to now allowing all methods that are supported by p.adjust
### Bug fixes
## Bug fixes
- various minor bug fixes
### Minor changes
## Minor changes
## GRaNIE 0.6 (2021-02-09)
# GRaNIE 0.6 (2021-02-09)
### Major changes
## Major changes
- significant speed improvements for the peak-FDR calculations and subsequent plotting
- TF-peak diagnostic plots now also show negatively correlated TF-peak statistics irrespective of whether they have been filtered out in the object / pipeline. This may be useful for diagnostic purposes to check whether excluding them is a sensible choice and to confirm the numbers are low
### Bug fixes
## Bug fixes
- Numbers for connections per correlation bin in the TF-peak diagnostic plots were wrong as they did not correctly differentiate between the different connection types in case multiple ones had been specified (e.g., expression and TF activity). This has been fixed.
### Minor changes
## Minor changes
## GRaNIE 0.5 (2021-02-02)
# GRaNIE 0.5 (2021-02-02)
first published package version
......@@ -5,9 +5,11 @@
"Welcome to the ", utils::packageName(), " package and thank you for using our software. This is ", utils::packageName(), " version ", utils::packageVersion(utils::packageName()),".\n",
"See the vignettes (type browseVignettes(\"", utils::packageName(), "\") or the help pages for how to use it for your analyses.\n",
"All project-related information, guidance, help, documentation and ways to contact us can be found here: https://grp-zaugg.embl-community.io/GRaNIE\n",
"You may also check the R help\n"
"All project-related information and ways to contact us can be found here: https://grp-zaugg.embl-community.io/GRaNIE\n"
)
packageStartupMessage(message)
......
### Gene Regulatory Network Inference including Enhancers: Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data
### GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks
*GRaNIE* (**G**ene **R**egul**a**tory **N**etwork **I**nference including **E**nhancers) is currently under active development. If you have questions, please do not hesitate to contact us (see below).
......@@ -6,7 +6,6 @@
*Towards a data-driven cell-type specific regulatory network including enhancers*
Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To
understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific
regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type
......
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<p class="section-desc"><p>Learn how to use the GRaNIE package with a full workflow example</p></p>
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<dl><dt><a href="workflow.html">Workflow example</a></dt>
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