Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
fe20684
commit c7668a9
Showing
10 changed files
with
4,940 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| Package: mixOmics | ||
| Type: Package | ||
| Title: Omics Data Integration Project | ||
| Version: 6.4.0 | ||
| Date: 2018-10-03 | ||
| Depends: R (>= 3.5.0), MASS, lattice, ggplot2 | ||
| Imports: igraph, rgl, ellipse, corpcor, RColorBrewer, parallel, | ||
| dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, utils | ||
| Suggests: BiocStyle, knitr, rmarkdown | ||
| Author: Kim-Anh Le Cao, Florian Rohart, Ignacio Gonzalez, Sebastien Dejean with key contributors Benoit Gautier, Francois Bartolo | ||
| and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet. | ||
| Maintainer: Kim-Anh Le Cao <kimanh.lecao@unimelb.edu.au> | ||
| Description: Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares. | ||
| License: GPL (>= 2) | ||
| URL: http://www.mixOmics.org | ||
| BugReports: https://bitbucket.org/klecao/package-mixomics/issues | ||
| Repository: Bioconductor | ||
| VignetteBuilder: knitr | ||
| Date/Publication: 2017-02-06 12:08:22 | ||
| Packaged: 2017-02-06 06:49:17 UTC; klecao | ||
| NeedsCompilation: no | ||
| LazyData: true | ||
| biocViews: Microarray, Sequencing, Metabolomics, Metagenomics, Proteomics, GenePrediction, MultipleComparison, Classification, Regression | ||
| RoxygenNote: 6.0.1.9000 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,185 @@ | ||
| 846c1611fd2d223c154c280186a17bed *DESCRIPTION | ||
| 1ae0316d01a8fb201505d564fd99bba3 *NAMESPACE | ||
| 66ad7d745c0bad14b70107ff1282d0df *NEWS | ||
| 2f85a1e402fc64261dd0047464b40205 *R/LOGOCV.R | ||
| b5ba704bc7398703c6ebe341636d89d6 *R/MCVfold.R | ||
| 2f07e018a307729f6b73d285c25f467b *R/bin.color.R | ||
| 488f794a9e87700a5192c7eb0e71dbdd *R/block.pls.R | ||
| 459ca87cba3d4bd55a7f00ac86acde08 *R/block.plsda.R | ||
| f50e64f26f2bde3073f955a86de57c32 *R/block.spls.R | ||
| f8c55b520038b2cb7599f3bae1b5ccce *R/block.splsda.R | ||
| 79acddb525061a13f59f6a4c687cea60 *R/check_entry.R | ||
| 8bf4ac78b0cbe36e4cffd0dc5630dd5b *R/cim.R | ||
| 5900ea90184b1914d9475e680818e33f *R/cimDiablo.R | ||
| 7556e32c753d47377ae8f756a3d0e567 *R/circosPlot.R | ||
| 592d398df8fccbc106e9c4573d20ba78 *R/color.GreenRed.R | ||
| ca2c8688d4b152927bb02d481da0138e *R/color.jet.R | ||
| 37f8bad1373e4dc6dabf0c3649c0ad88 *R/color.mixo.R | ||
| 11f0fcd07ee2ca13f4a5cb569bbcdd51 *R/color.spectral.R | ||
| 91cbcdee2272b21ec33eeb82d08c5f58 *R/explained_variance.R | ||
| 396a0a7d0a1d40e87dad34fb6de43835 *R/ica.def.par.R | ||
| 4e849761115f3890ae039c05a83192cb *R/image.tune.rcc.R | ||
| 68b696ea856bf8b40966d7097274676a *R/imageMap.R | ||
| cbfa2c1e1f217c38f5bfd317a2da0d59 *R/imgCor.R | ||
| ba8fcfed3989ffc44e71c14c333fbbb1 *R/internal_graphicModule.R | ||
| 54f69d65e21f81a4bd6a6600989eb219 *R/internal_mint.block.R | ||
| 45da0c70dfffa2eaacc05e35333803f3 *R/internal_mint.block_helpers.R | ||
| fcf9cc656571643228f03af48e136492 *R/internal_predict.DA.R | ||
| 6afc689854df854a6eca4f4251210317 *R/internal_wrapper.mint.R | ||
| d97011b86383bfffef800c1ea267aa7d *R/internal_wrapper.mint.block.R | ||
| 841ab59c76cfa5fd1bdf84485d07611b *R/ipca.R | ||
| 621a2be73b95810ada02354424d9885d *R/mat.rank.R | ||
| d80abf063fa3013532b2295db0c5f331 *R/mint.block.pls.R | ||
| c8646103956430ed69a0fc74cecd8506 *R/mint.block.plsda.R | ||
| d7de90ec85950f7f898cd85402f83b98 *R/mint.block.spls.R | ||
| 1412611648790e23287f79fa6a393903 *R/mint.block.splsda.R | ||
| 6444f85a11e24edd6722d446a0605ffd *R/mint.pls.R | ||
| 21bb624e5e28dddf99b41ffb1d9e4205 *R/mint.plsda.R | ||
| 2719de678362f61257322df8d47cdae8 *R/mint.spls.R | ||
| b89f82a2e823b7cd43a2e8e2607c4ca0 *R/mint.splsda.R | ||
| 9c0b2e8c8b9ad7da272187b18b9d3ef9 *R/mixOmics.R | ||
| 682e27bf8b6f3a9c6d3573edcb6598b0 *R/multilevel.R | ||
| 347ba06b882532a8e56521eff82ca32f *R/nearZeroVar.R | ||
| 82867e0bb51b4d2980a82213a48e0b72 *R/network.R | ||
| c19b0b53c31867af82fb9916bc8fc22c *R/nipals.R | ||
| b4ef9a82dbf43a0982fc06fad77fcb19 *R/pca.R | ||
| bab2aff1b6e28253cacb01224a540db2 *R/pcasvd.R | ||
| 465475c32c3a25ef0562529cd3fff547 *R/perf.R | ||
| 7c64fb6a38f38e564cada2ca7beec964 *R/perf.diablo.R | ||
| 562ea17ea69526f1b491534fd1f9ca52 *R/perf.mint.splsda.R | ||
| 08dfd346d4c836b790750331dfe7c027 *R/plot.pca.R | ||
| cf8c4b004ed66f0a88764f0e75abe26d *R/plot.perf.R | ||
| a518ca15017cbe0b95cd7becf1f26711 *R/plot.rcc.R | ||
| 745d7ff8ac88319c3859df1bb9c4d9c9 *R/plotArrow.R | ||
| bb35e705461d78dbc1da365de7f0f43b *R/plotContrib.R | ||
| c7ccfd4a249d4b9ee4d2b27d3da06596 *R/plotDiablo.R | ||
| 2dd685be3feaebc58e8d8c36973853eb *R/plotIndiv.R | ||
| c22f5d9dfaf7093d54b6f44f58f9132e *R/plotIndiv.mint.R | ||
| 1d786bebfd36ecedaa1ec4cd176b623d *R/plotIndiv.pca.R | ||
| bc57d74e2a93e9eb864b1872942109dd *R/plotIndiv.pls.R | ||
| 1cde1e7055c18f745341f27fba862bfc *R/plotIndiv.sgcca.R | ||
| 11c94012ebde07aa71eedaec5df0c30e *R/plotLoadings.R | ||
| 2fa2686949245387e576078ec6a6c003 *R/plotLoadings.mint.spls.R | ||
| d95e80386a42cb66683555ba9f934c05 *R/plotLoadings.mint.splsda.R | ||
| 5631e4515fe6c1adb5cade7690eca5a0 *R/plotLoadings.spls.R | ||
| ec442acd6f012ad5e21dd8c7fc3b0327 *R/plotLoadings.splsda.R | ||
| 542f73440765d63e09476703e35a2372 *R/plotVar.R | ||
| 91781d77d8d0b4fbf130607e1a833411 *R/pls.R | ||
| 0119a9b4478ca843179f80732c36826f *R/plsda.R | ||
| 89fdd5e701b46ebc1663a5c275475b8f *R/predict.mint.block.pls.R | ||
| 3ffb29454b512dfd955545598e312d08 *R/print.methods.R | ||
| b9503565f9fff2d27bba8da3d6159093 *R/rcc.R | ||
| f8ef595f93c3dbf60b7840530b5b0594 *R/scatterutil.R | ||
| 23325759abe5cab967a27c5b90977b9b *R/selectVar.R | ||
| 6a9cc5f8f417bf8949e5ab654d725af0 *R/sipca.R | ||
| f83a72110bd90ec01f5208f99de705f4 *R/spca.R | ||
| 158108d09d673af7e1b6dad0743faf38 *R/spls.R | ||
| 10eec5ad3cffd2cc567383891c0162db *R/splsda.R | ||
| eb45db78313cfa6a8eafef9ef9f3be4c *R/summary.R | ||
| 41ac660ef78c18b27dd89303691d49a9 *R/tune.R | ||
| a052f8dea245aed10c098230be801d27 *R/tune.mint.splsda.R | ||
| 0efe88976a0838a8a951d12b64d01e1a *R/tune.multilevel.R | ||
| 62776d04e3cf06601c254646d4d3a602 *R/tune.pca.R | ||
| d5e843029babe6b7080f2fe5d311ba6a *R/tune.rcc.R | ||
| c6896a3a46b7b5108469f74ac06f48c0 *R/tune.splsda.R | ||
| 6dd02c8f836b7813e164c0314ddd9b3c *R/tune.splslevel.R | ||
| b67a96184045f73f83ea27ed3d6f648a *R/unmap.R | ||
| d37bcd20fc0b15d0f3144348dea020a1 *R/vip.R | ||
| 97ca39a800401b324c63370ee71582c0 *R/withinVariation.R | ||
| 4a426f946bf58bdd863a32bdd17bd5a9 *R/wrapper.ilr.R | ||
| 868ac6ab68c487f862ea37101dd8c77b *R/wrapper.rgcca.R | ||
| 15a109953a56cd936cd49305abb38974 *R/wrapper.sgcca.R | ||
| a2aa9bee7830adbf5e161e4156bd3c78 *R/zzz.R | ||
| 738363883dc01b7f5c73d302a3f59f36 *README | ||
| 17dd1e715e5503db5646913cab356775 *data/Koren.16S.rda | ||
| 3910a4e4c17072f14c563716a2d22e12 *data/breast.TCGA.rda | ||
| 82288f46638f003b7717b05fd85e15c8 *data/breast.tumors.rda | ||
| 47e2e9e4c90c6ee0b2c386c7e7a30684 *data/datalist | ||
| 1fc34b1126640c5de7c0faa1a30d291e *data/diverse.16S.rda | ||
| 097058f459bd3d5e3fcab33d1b6c69ee *data/linnerud.rda | ||
| 54b811ebff2d6be711082463998a90d9 *data/liver.toxicity.rda | ||
| e1e40590258f07da92d85dff2fc7141f *data/multidrug.rda | ||
| 21c616379af72e996a2d4eba0aa0162f *data/nutrimouse.rda | ||
| 6067aaaad7b3a1d351cb11326fd6b7f9 *data/srbct.rda | ||
| 5b1b145f94452c771d69d0ee24fa8282 *data/stemcells.rda | ||
| 4442e68208bf73811665dae3e668d12b *data/vac18.rda | ||
| 83265f89993f1b1f4dbf5b3587d56275 *data/vac18.simulated.rda | ||
| 2708b61234e7de185fd314ede9c408d0 *data/yeast.rda | ||
| dfc2d84faaf103ac6821d6ee2f7eaed3 *man/Koren.16S.Rd | ||
| aa18d8fce39893bbf71c1d4558673d74 *man/block.pls.Rd | ||
| 546e5612bf86f6fab0445d1133a3ccf8 *man/block.plsda.Rd | ||
| e3e52ac69712b5bac6364d6db9bb1f95 *man/block.spls.Rd | ||
| 98b7d1859acdf702aa3e0f61f5120805 *man/block.splsda.Rd | ||
| 070db2889adae4b674b4d727e9b0fc80 *man/breast.TCGA.Rd | ||
| 0edd1a843cf8ad0563c4db6f9c12a314 *man/breast.tumors.Rd | ||
| c5a4c4036f860b356d902ecf857080cd *man/cim.Rd | ||
| 029547adcf1e321c633845e186931309 *man/cimDiablo.Rd | ||
| 8160bf239e444f638c1835aae4aa915d *man/circosPlot.Rd | ||
| 909fb39a5a4b842d439451b7a72c865e *man/colors.Rd | ||
| 0578e9e5e60289a9db3d679f3f08aae4 *man/diverse.16S.Rd | ||
| 1e5a4dd8621b829470e781bf3776a05e *man/estim.regul.Rd | ||
| aa01173eb45d3ed8803db54b84f324c5 *man/explained_variance.Rd | ||
| be7cb77754e1da1ea499d1d18134f24b *man/image.estim.regul.Rd | ||
| bf5d54f211f46c6e5c66ee2389661614 *man/image.tune.rcc.Rd | ||
| 91e099b0de3e6b5025d0ce7e7f5f6399 *man/imgCor.Rd | ||
| 2aefdf1f6f93a1132cfcdf6c20a827e2 *man/ipca.Rd | ||
| e1d5acdf822cc82d616c61a1a5b7fab8 *man/linnerud.Rd | ||
| 52d3c2bad0bbcf9ef9d0fac1caa4824c *man/liver.toxicity.Rd | ||
| e768aed3523191780fd5da968183094d *man/logratio.transfo.Rd | ||
| 401cda2f25adcc43ae2798ed7570fa66 *man/map.Rd | ||
| 68f14a88c835e30f9edc7115d3c9561f *man/mat.rank.Rd | ||
| eab285c84bf122821ba8df6f0bd0779a *man/mint.block.pls.Rd | ||
| 16609bce248c8a26b133a9c181ebbf9c *man/mint.block.plsda.Rd | ||
| f6260986eeaea076227498688cc272c2 *man/mint.block.spls.Rd | ||
| ed1b4330e05a4b63898f5f2942145e35 *man/mint.block.splsda.Rd | ||
| 9578260a1b1d47f6f5595a0a4983eba2 *man/mint.pls.Rd | ||
| 0a074bf2a73764125504ce79ce5c5ee2 *man/mint.plsda.Rd | ||
| 301ea784d7bafb98083bcf94628fe517 *man/mint.spls.Rd | ||
| a6dcd4e85139b486b120ec4be69aff08 *man/mint.splsda.Rd | ||
| c89d7c68512f90e21187002d3ea12374 *man/mixOmics.Rd | ||
| cf6ae3e3d15e0cb69f8a30d8fc512b70 *man/multidrug.Rd | ||
| c27923f069fe6616e816fc93ce0b75cb *man/multilevel.Rd | ||
| 5e00d2c31441f02345e0ff874e541e92 *man/nearZeroVar.Rd | ||
| 6a3befad8cec1cff7d9493216ea0e866 *man/network.Rd | ||
| e08c7e127abbbf227d3458991fea3af3 *man/nipals.Rd | ||
| 645886261bd6220ec1af461d56ad4580 *man/nutrimouse.Rd | ||
| 0d976e857b13346c0ab5393a65e01a2f *man/pca.Rd | ||
| d57f8c042928e2b007d7d316c17ea7bb *man/pcatune.Rd | ||
| a139c1c438df256281560fddd7492f69 *man/perf.Rd | ||
| 5e80339fc248625c3973ae78debe2033 *man/plot.perf.Rd | ||
| 1b1bc58bdba3f275da46dfdf908932c6 *man/plot.rcc.Rd | ||
| 72a52d608a93af7394692e34e3bab181 *man/plotArrow.Rd | ||
| d6d06b937b318b41a0126db2c653d89e *man/plotContrib.Rd | ||
| cd0dd7e8f9dc0941f273d3d611916871 *man/plotDiablo.Rd | ||
| 1090740af6be36e87ea7f4f769a3469a *man/plotIndiv.Rd | ||
| 1874b8b4e1e91d36c45544065aae50e2 *man/plotLoadings.Rd | ||
| a623a32d64d1254e1dc5bb01e9d088c3 *man/plotVar.Rd | ||
| ef94ee72f47fef08e5422801cccc30fe *man/pls.Rd | ||
| 4b69c7304023eac7eb2bb06eac8fc533 *man/plsda.Rd | ||
| 9a9e26655e802b7c21d01d23ecbb1773 *man/predict.Rd | ||
| bd1d57202d2109c85c861dc18c92fa20 *man/print.methods.Rd | ||
| b00c55f9240ced4db97d7b499a9beabd *man/rcc.Rd | ||
| 8105165a19bd1c55035e5b678612cc0f *man/scatterutil.Rd | ||
| cc78ebd12beaf57e432fa3eff16d0b7f *man/selectVar.Rd | ||
| 3f72ab33f7d1511943adde4cd8d4b1f7 *man/sipca.Rd | ||
| f7795fafd68bd042a8a487caa441f5bd *man/spca.Rd | ||
| 8d4e8bb362532e947660da498b0b080e *man/spls.Rd | ||
| 99767b9f0b3cb717966e73ac9d19fb54 *man/splsda.Rd | ||
| 1d2dce9d413f1f68992559ac734bdd7c *man/srbct.Rd | ||
| 5ae6826d6c74bfddba34838bf43f803c *man/stemcells.Rd | ||
| b139f644a6ea0bb34a643e0fe05a1631 *man/study_split.Rd | ||
| e0bcb1774c02467042070164684fbd4b *man/summary.Rd | ||
| b809c66d16cd68ad43190118b4b5409c *man/tune.Rd | ||
| 8987a31a6135d78aef2daa836a36e096 *man/tune.mint.splsda.Rd | ||
| 320bacb435dbbbe1e472eab8f4639d0c *man/tune.multilevel.Rd | ||
| 86a6c9644a7ceae40c33083a38af347b *man/tune.pca.Rd | ||
| fafd3e73c4e96f427ddfabdc56be325f *man/tune.rcc.Rd | ||
| 21f853524b2bbb5787d09f7e6d646a18 *man/tune.splsda.Rd | ||
| c19cbed910b4014defc25e302b4294f2 *man/unmap.Rd | ||
| 7e3eec557969f0c1c030767c6d3a6043 *man/vac18.Rd | ||
| 251f5c7fb80a9452cb20cd306fc8347e *man/vac18.simulated.Rd | ||
| f91e2317d0c43b528327ca469dac3666 *man/vip.Rd | ||
| ba2a971073117563d632e9293579e9ff *man/withinVariation.Rd | ||
| 65e5ea9e8b5f697d6efb919c2e9e0c6e *man/wrapper.rgcca.Rd | ||
| 3531e6a53eee0bd5bc539d6e198d7fd7 *man/wrapper.sgcca.Rd | ||
| 686391e9e681d9a7eb13ed41370f2fe0 *man/yeast.Rd |
Oops, something went wrong.