From 0f06727f09506955a99da7398a50507b026ad753 Mon Sep 17 00:00:00 2001 From: marouenbg Date: Tue, 23 Nov 2021 11:45:05 -0500 Subject: [PATCH 001/199] add bioc information --- DESCRIPTION | 10 +++++----- README.md | 12 ++++++++++++ 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3fd7cc2c..35f33ee0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,11 +1,11 @@ Package: netZooR -Title: Integrate methods: PANDA, LIONESS, CONDOR, ALPACA, SAMBAR, MONSTER, OTTER, EGRET, and YARN into one workflow +Title: netZooR integrates tools for the inference and analysis of gene regulatory networks. Version: 0.99.85 Date: 2021-09-20 -Authors@R: c(person("Tian", "Wang", +Authors@R: c(person("Marouen", "Ben Guebila", + email = "benguebila@hsph.harvard.edu", role = c("aut","cre")), + person("Tian", "Wang", email = "tian.wang@bc.edu", role = c("aut")), - person("Marouen", "Ben Guebila", - email = "marouen.b.guebila@gmail.com", role = c("aut","cre")), person("John", "Platig", email="john.platig@channing.harvard.edu",role="aut"), person("Marieke", "Kuijjer", @@ -16,7 +16,7 @@ Authors@R: c(person("Tian", "Wang", email = "rburkholz@hsph.harvard.edu",role = "aut"), person("Deborah", "Weighill", email = "",role = "aut")) -Description: PANDA(Passing Attributes between Networks for Data Assimilation) is a message-passing model to reconstruction gene regulatory network. It integrates multiple sources of biological data, including protein-protein interaction data, gene expression data, and sequence motif information to reconstruct genome-wide, condition-specific regulatory networks.[(Glass et al. 2013)]. LIONESS(Linear Interpolation to Obtain Network Estimates for Single Samples) is a method to estimate sample-specific regulatory networks by applying linear interpolation to the predictions made by existing aggregate network inference approaches. CONDOR(COmplex Network Description Of Regulators)is a bipartite community structure analysis tool of biological networks, especially eQTL networks, including a method for scoring nodes based on their modularity contribution.[(Platig et al. 2016). ALPACA(ALtered Partitions Across Community Architectures) is a method for comparing two genome-scale networks derived from different phenotypic states to identify condition-specific modules.[(Padi and Quackenbush 2018)]. This package integrates pypanda--the Python implementation of PANDA and LIONESS(https://github.com/davidvi/pypanda),the R implementation of CONDOR(https://github.com/jplatig/condor) and the R implementation of ALPACA (https://github.com/meghapadi/ALPACA) into one workflow. Each tool can be call in this package by one function, and the relevant output could be accessible in current R session for downstream analysis. +Description: PANDA (Passing Attributes between Networks for Data Assimilation) is a message-passing algorithm to reconstruct gene regulatory network. It integrates multiple sources of biological data, including protein-protein interaction data, gene expression data, and sequence motif information to reconstruct genome-wide, condition-specific regulatory networks.[(Glass et al. 2013)]. LIONESS(Linear Interpolation to Obtain Network Estimates for Single Samples) is a method to estimate sample-specific regulatory networks by applying linear interpolation to the predictions made by existing aggregate network inference approaches. CONDOR(COmplex Network Description Of Regulators)is a bipartite community structure analysis tool of biological networks, especially eQTL networks, including a method for scoring nodes based on their modularity contribution.[(Platig et al. 2016). ALPACA(ALtered Partitions Across Community Architectures) is a method for comparing two genome-scale networks derived from different phenotypic states to identify condition-specific modules.[(Padi and Quackenbush 2018)]. This package integrates pypanda--the Python implementation of PANDA and LIONESS(https://github.com/davidvi/pypanda),the R implementation of CONDOR(https://github.com/jplatig/condor) and the R implementation of ALPACA (https://github.com/meghapadi/ALPACA) into one workflow. Each tool can be call in this package by one function, and the relevant output could be accessible in current R session for downstream analysis. Depends: R (>= 4.1.0), igraph, reticulate, diff --git a/README.md b/README.md index 7d259ad7..582a1029 100644 --- a/README.md +++ b/README.md @@ -79,6 +79,18 @@ remotes::install_github("netZoo/netZooR", build_vignettes = TRUE) library(netZooR) ``` +netZooR is also available through Biocondcutor + +```r +if (!requireNamespace("BiocManager", quietly = TRUE)) + install.packages("BiocManager") + +# The following initializes usage of Bioc devel +BiocManager::install(version='devel') + +BiocManager::install("netZooR") +``` + For more details please refer to the [documentation website](https://netzoo.github.io/netZooR/). This package will invoke Python programming language in R environment through [reticulate](https://rstudio.github.io/reticulate/) package, by default setting there is no additional configuration needed. From 768a1988f56d4c977e44ce2aefc254d5590edddd Mon Sep 17 00:00:00 2001 From: marouenbg Date: Tue, 23 Nov 2021 21:18:00 -0500 Subject: [PATCH 002/199] update website --- .gitignore | 3 + README.md | 10 +- docs/404.html | 4 +- docs/CONDUCT.html | 4 +- docs/LICENSE-text.html | 4 +- docs/articles/ALPACA.html | 8 +- docs/articles/ApplicationinGTExData.html | 6 +- docs/articles/ApplicationwithTBdataset.html | 22 +- .../figure-html/unnamed-chunk-8-1.png | Bin 875869 -> 876097 bytes docs/articles/CONDOR.html | 19 +- .../figure-html/unnamed-chunk-10-1.png | Bin 31555 -> 30624 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 46536 -> 45507 bytes docs/articles/EGRET_toy_example.html | 4 +- .../LionessApplicationinGTExData.html | 38 +- .../figure-html/unnamed-chunk-6-1.png | Bin 205349 -> 204592 bytes .../figure-html/unnamed-chunk-9-1.png | Bin 210201 -> 214253 bytes docs/articles/MONSTER.html | 494 +++++++++--------- .../figure-html/unnamed-chunk-10-1.png | Bin 297793 -> 300317 bytes .../figure-html/unnamed-chunk-11-1.png | Bin 291183 -> 312746 bytes .../figure-html/unnamed-chunk-13-1.png | Bin 125039 -> 120265 bytes docs/articles/SAMBAR.html | 4 +- docs/articles/TutorialOTTER.html | 56 +- .../figure-html/unnamed-chunk-15-1.png | Bin 170905 -> 187357 bytes docs/articles/index.html | 4 +- docs/articles/pandaR.html | 4 +- .../articles/pandaRApplicationinGTExData.html | 68 +-- .../figure-html/unnamed-chunk-14-1.png | Bin 176296 -> 168210 bytes docs/articles/yarn.html | 10 +- docs/authors.html | 8 +- docs/index.html | 47 +- docs/pkgdown.yml | 2 +- docs/reference/alpaca.html | 8 +- .../alpacaCommunityStructureRotation.html | 4 +- docs/reference/alpacaDeltaZAnalysis.html | 4 +- .../alpacaDeltaZAnalysisLouvain.html | 4 +- docs/reference/alpacaExtractTopGenes.html | 8 +- docs/reference/alpacaGOtabtogenes.html | 4 +- docs/reference/alpacaRotationAnalysis.html | 4 +- .../alpacaRotationAnalysisLouvain.html | 4 +- docs/reference/alpacaTestNodeRank.html | 4 +- docs/reference/alpacaTopEnsembltoTopSym.html | 4 +- docs/reference/alpacaWBMlouvain.html | 4 +- .../reference/alpacacomputeDWBMmatmscale.html | 4 +- docs/reference/alpacacomputeWBMmat.html | 4 +- docs/reference/alpacagenlouvain.html | 4 +- docs/reference/alpacagotogenes.html | 4 +- docs/reference/alpacalisttogo.html | 4 +- docs/reference/alpacametanetwork.html | 4 +- docs/reference/alpacanodetogene.html | 4 +- docs/reference/alpacasimulateNetwork.html | 4 +- docs/reference/alpacatidyconfig.html | 4 +- docs/reference/condorCluster.html | 4 +- docs/reference/condorCoreEnrich.html | 4 +- docs/reference/condorMatrixModularity.html | 4 +- docs/reference/condorModularityMax.html | 4 +- docs/reference/condorPlotCommunities.html | 4 +- docs/reference/condorPlotHeatmap.html | 4 +- docs/reference/condorQscore.html | 4 +- docs/reference/createCondorObject.html | 4 +- docs/reference/createPandaStyle.html | 4 +- docs/reference/exon.size.html | 4 +- docs/reference/genes.html | 4 +- docs/reference/index.html | 4 +- docs/reference/lioness.html | 4 +- docs/reference/lionessPy.html | 4 +- docs/reference/monster.html | 50 +- docs/reference/monsterBereFull.html | 4 +- docs/reference/monsterCalculateTmPvalues.html | 4 +- docs/reference/monsterCheckDataType.html | 4 +- docs/reference/monsterGetTm.html | 4 +- docs/reference/monsterHclHeatmapPlot.html | 4 +- docs/reference/monsterMonsterNI.html | 8 +- .../reference/monsterPlotMonsterAnalysis.html | 50 +- .../monsterPrintMonsterAnalysis.html | 50 +- docs/reference/monsterRes.html | 4 +- .../monsterTransformationMatrix.html | 12 +- docs/reference/monsterTransitionPCAPlot.html | 4 +- docs/reference/monsterdTFIPlot.html | 4 +- .../monstertransitionNetworkPlot.html | 4 +- docs/reference/mut.ucec.html | 4 +- docs/reference/otter.html | 4 +- docs/reference/pandaPy.html | 4 +- docs/reference/pandaToAlpaca.html | 20 +- docs/reference/pandaToCondorObject.html | 4 +- docs/reference/runEgret.html | 8 +- docs/reference/sambar.html | 4 +- docs/reference/sambarConvertgmt.html | 4 +- docs/reference/sambarCorgenelength.html | 4 +- docs/reference/sambarDesparsify.html | 4 +- docs/reference/small1976.html | 4 +- docs/reference/sourcePPI.html | 4 +- docs/reference/visPandaInCytoscape.html | 4 +- docs/reference/yeast.html | 4 +- 93 files changed, 662 insertions(+), 583 deletions(-) diff --git a/.gitignore b/.gitignore index 089271c4..30b75b1e 100644 --- a/.gitignore +++ b/.gitignore @@ -32,3 +32,6 @@ tests/testthat/*.txt tests/testthat/*.vcf /doc/ /Meta/ +vignettes/*.npy +docs/*.npy +docs/reference/*.npy diff --git a/README.md b/README.md index 582a1029..771bfff5 100644 --- a/README.md +++ b/README.md @@ -64,6 +64,10 @@ The package also integrates additional functions to: - Most of plotting function can be realized by functions in [igraph](https://igraph.org/redirect.html), which will be loaded with netZooR through `library(netZooR)`. Some plotting functions like `vis.panda.in.cytoscape()` and `vis.diff.panda.in.cytoscape()` are able to plot interactive PANDA networks in [Cytoscape](https://cytoscape.org/), but installation of Cytoscape is required before using these plotting functions. Also, please make sure that Cytoscape is open when these functions are called. +### Installation + +#### Using devtools/remotes + ```r # install.packages("devtools") # install netZooR pkg with vignettes, otherwise remove the "build_vignettes = TRUE" argument. @@ -79,7 +83,9 @@ remotes::install_github("netZoo/netZooR", build_vignettes = TRUE) library(netZooR) ``` -netZooR is also available through Biocondcutor +#### Using Bioconductor + +netZooR is also available through [Bioconductor](https://bioconductor.org/packages/netZooR) ```r if (!requireNamespace("BiocManager", quietly = TRUE)) @@ -93,6 +99,8 @@ BiocManager::install("netZooR") For more details please refer to the [documentation website](https://netzoo.github.io/netZooR/). +### Python binding + This package will invoke Python programming language in R environment through [reticulate](https://rstudio.github.io/reticulate/) package, by default setting there is no additional configuration needed. Configuring which version of Python to use , here in netZooR, Python 3.X is required. More details can be found [here](https://cran.r-project.org/web/packages/reticulate/vignettes/versions.html). diff --git a/docs/404.html b/docs/404.html index 293bd9bf..709177b0 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ netZooR - 0.99.81 + 0.99.85 @@ -171,7 +171,7 @@

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