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Update authors #326

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091647a
fix monster error
marouenbg Mar 14, 2023
2368932
update documentation
marouenbg Mar 23, 2023
7e7e794
remove monster tests
marouenbg Mar 24, 2023
09f394f
reduce monstr test
marouenbg Mar 27, 2023
625a4ed
update documentation
marouenbg Mar 28, 2023
bb77e10
remove diffedge example
marouenbg Mar 31, 2023
e001f17
reduce monster tests
marouenbg Apr 3, 2023
5884b00
remove spider example
marouenbg Apr 4, 2023
89f94cd
update monster examples
marouenbg Apr 6, 2023
3c388ff
remove lioness tests
marouenbg Apr 8, 2023
9f1962c
remove pada tests
marouenbg Apr 10, 2023
3343f6b
add citation
marouenbg May 24, 2023
36938c0
Merge remote-tracking branch 'upstream/devel' into devel
marouenbg May 24, 2023
06156fd
Merge remote-tracking branch 'upstream/devel' into devel
marouenbg May 31, 2023
86e297d
Merge remote-tracking branch 'upstream/devel' into devel
marouenbg Sep 2, 2023
1847f8c
Merge remote-tracking branch 'upstream/devel' into devel
marouenbg Sep 21, 2023
a87374f
Merge remote-tracking branch 'upstream/devel' into devel
marouenbg Nov 18, 2023
ed1100f
Merge remote-tracking branch 'upstream/devel' into devel
marouenbg Feb 20, 2024
3290fa3
Merge remote-tracking branch 'upstream/devel' into devel
marouenbg Mar 8, 2024
af16e51
Merge remote-tracking branch 'upstream/devel'
marouenbg Mar 8, 2024
4b7ad2a
Merge branch 'master' into devel
marouenbg Mar 8, 2024
90c6acd
Merge branch 'devel' of https://github.com/marouenbg/netZooR into devel
marouenbg Jul 26, 2024
2d4758a
Merge remote-tracking branch 'upstream/devel' into devel
marouenbg Jul 26, 2024
d8b8c99
add Taras info
marouenbg Jul 26, 2024
266789e
Update test-monster.R
marouenbg Jul 26, 2024
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18 changes: 11 additions & 7 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
Package: netZooR
Type: Package
Title: Unified methods for the inference and analysis of gene regulatory networks
Version: 1.5.17
Date: 2024-02-29
Authors@R: c(person("Marouen", "Ben Guebila",
email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")),
Version: 1.6.0
Date: 2024-07-26
Authors@R: c(person("Tara", "Eicher",
email = "teicher@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0003-1809-4458")),
person("Marouen", "Ben Guebila",
email = "benguebila@hsph.harvard.edu", role = c("aut"), comment = c(ORCID = "0000-0001-5934-966X")),
person("Tian", "Wang",
email = "tian.wang@bc.edu", role = c("aut"), comment = c(ORCID = "0000-0002-2767-3243")),
person("John", "Platig",
Expand All @@ -15,11 +17,13 @@ Authors@R: c(person("Marouen", "Ben Guebila",
email = "mpadi@email.arizona.edu", role = "aut", comment = c(ORCID = "0000-0002-3446-4562")),
person("Rebekka", "Burkholz",
email = "rburkholz@hsph.harvard.edu",role = "aut"),
person("Des", "Weighill",
person("Des", "Weighill",
email = "",role = "aut", comment = c(ORCID = "0000-0003-4979-5871")),
person("Kate", "Shutta",
person("Chen", "Chen",
email = "",role = "aut", comment = c(ORCID = "0000-0002-8042-7201")),
person("Kate", "Shutta",
email = "",role = "aut", comment = c(ORCID = "0000-0003-0402-3771")))
Maintainer: Marouen Ben Guebila <marouen.b.guebila@gmail.com>
Maintainer: Tara Eicher <teicher@hsph.harvard.edu>
Description: netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.
Depends: R (>= 4.2.0),
igraph,
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8 changes: 8 additions & 0 deletions NEWS.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,11 @@
CHANGES IN VERSION 1.6.0
--------------------------

- New method: COBRA for batch-effect correction in correlation networks
- New method: BLOBFISH for estimating null models for gene regulatory networks
- New method: TIGER finds transcription factor activity using a Bayesian approach


CHANGES IN VERSION 1.3.2
--------------------------

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