Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

github.com/YuLab-SMU/ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees
https://github.com/YuLab-SMU/ggtree

Bumped versions of all packages prior to creating 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@109589 ...

cb61c7f0e0a71b0ba54bf192b78f307aa8753c35 authored about 9 years ago by Dan Tenenbaum <[email protected]>
update news

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@109354 b...

0003d656dec29fd79cb9f62ce2b328860832b157 authored over 9 years ago by Guangchuang Yu <[email protected]>
update news

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@109354 bc3139a8-6...

23bd4a6b356f42c7a2dbd6ea1a8090a20ade02b8 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
update comment

851785c153aebbac0bc62b79956dbce6e83b396c authored over 9 years ago by GuangchuangYu <[email protected]>
support hyphy output of ancestral sequences that is in phylip sequential format (no TAXALABELS block available) <2015-10-07, Wed>

6032a08927af2db4dca096a40423b78c1f0209b8 authored over 9 years ago by GuangchuangYu <[email protected]>
add r8s and raxml support

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@109098 bc3139a8-6...

75f08f2b89a838577ad6ab507a642194bf7de478 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
add r8s and raxml support

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@109098 b...

341b0ee82412cfde7e0e7e71cb86d940598f94e3 authored over 9 years ago by Guangchuang Yu <[email protected]>
fixed bug in geom_tiplab when x contains NA (eg, removing by collapse function) <2015-10-01, Thu>

ea9d66164c93c639ea6989a4bc693760059cfdae authored over 9 years ago by GuangchuangYu <[email protected]>
add blog link

6ac1ca774a9f9e687136b5d7a4e1ff31864b1a90 authored over 9 years ago by GuangchuangYu <[email protected]>
tiny typo in vignette

405903cb00ea50b429dc6c90c34f0c90e1e41748 authored over 9 years ago by GuangchuangYu <[email protected]>
Add a Bitdeli badge to README

198c71d4b1ba43dc44b28346e53976386fc1b5a8 authored over 9 years ago by Bitdeli Chef <[email protected]>
Update README.md

25f64529135a424ef332c9620b8aa6d1419631ce authored over 9 years ago by Guangchuang Yu <[email protected]>
Merge pull request #11 from bitdeli-chef/master

Add a Bitdeli Badge to README

6780daaed149425df9dc98d90c86abcdbb7e1ad6 authored over 9 years ago by Guangchuang Yu <[email protected]>
new geom_hilight implementation

48a725aef0c5ced5baa300d2287054fecac3729e authored over 9 years ago by GuangchuangYu <[email protected]>
add doc link

9f7c47480b04c9843a94b056aeba9dad9d17a7b8 authored over 9 years ago by GuangchuangYu <[email protected]>
update %add2%

c74f3fe3d2b0ec092b31381bf9d72359a35ea059 authored over 9 years ago by GuangchuangYu <[email protected]>
bug fixed in %add2%, if node available use node, otherwise use label <2015-09-04, Fri>

099a43ef1af145f1936ed757ba2e39cb425b1c06 authored over 9 years ago by GuangchuangYu <[email protected]>
bug fixed of subview for considering aes mapping of x and y <2015-09-03, Thu>

799b998cbe52e617f0e3baf504c23d8cd54ca9c6 authored over 9 years ago by GuangchuangYu <[email protected]>
bug fixed

d381db69d698bdec7c24902f1ed0dad55cb8e225 authored over 9 years ago by GuangchuangYu <[email protected]>
r8s methods

7ef6e3ff74b19d901fdf507ce641586dbb580095 authored over 9 years ago by GuangchuangYu <[email protected]>
methods for r8s

2b610370e1837f6fb5110e0762621f97fdd9f31e authored over 9 years ago by GuangchuangYu <[email protected]>
read.r8s

11b711b35dc6aa20ba2e3b1f76beee66121e6f63 authored over 9 years ago by GuangchuangYu <[email protected]>
bug fixed in multiPhylo

7246dd8d7e487481fd355a683c407d6ac51dec3c authored over 9 years ago by GuangchuangYu <[email protected]>
r8s class definition

aafeaf45c0a35dfe2c2c1e82119d7adb3aa03d0a authored over 9 years ago by GuangchuangYu <[email protected]>
r8s files

21e07830ee32819fafb551b4c61f105137d19034 authored over 9 years ago by GuangchuangYu <[email protected]>
raxml files

03aa734089c469cdab6b06de5f7f26346ef52dff authored over 9 years ago by GuangchuangYu <[email protected]>
remove png file

b82ce5a0f486d0ec6a585599836ebda825afe7d2 authored over 9 years ago by GuangchuangYu <[email protected]>
o update scale_x_ggtree to support Date as x-axis <2015-09-01, Tue>

5c37905c768e34715bed62c91a57a0110488126c authored over 9 years ago by GuangchuangYu <[email protected]>
remove time_scale and add mrsd parameter

562427afc6f61636c1a6358f45426eae9f0b1f7b authored over 9 years ago by GuangchuangYu <[email protected]>
add example file of RAxML

da752de7510c528c322a78420244ad1923a8e099 authored over 9 years ago by GuangchuangYu <[email protected]>
fortify.raxml method

9061e5cafc92877f701353bf75d58bb55b375876 authored over 9 years ago by GuangchuangYu <[email protected]>
plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom, and show methods

7c0fcec555313ac2914eb7279227fc6f79a0b945 authored over 9 years ago by GuangchuangYu <[email protected]>
raxml class and read.raxml function

7ebbb7bcf76cfb9a62aa68a38cd3359a309eddf7 authored over 9 years ago by GuangchuangYu <[email protected]>
fixed edgeNum2nodeNum

4cf84f3e9fb93d96ee9afbe0b17fb09a381214e0 authored over 9 years ago by GuangchuangYu <[email protected]>
add external doc

7b0079ae4c6e118aa6fa974259b32d70ab0a5b34 authored over 9 years ago by Guangchuang Yu <[email protected]>
support multiPhylo for other tree objects

1a410f7d300e8615e0f7ed6cd1db13afa90f0b7c authored over 9 years ago by Guangchuang Yu <[email protected]>
multiPhylo

da508dc1391716da7293dcf755ce21b48698b5a0 authored over 9 years ago by GuangchuangYu <[email protected]>
remove dependency of phytools and EBImage

e7af7c6d178efca56c7edef101ccaa8c83242005 authored over 9 years ago by GuangchuangYu <[email protected]>
revert to previous version for compatible with CRAN version of ggplot2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107950 b...

8d490ae507d65d8dd319f54ccf579f01245bf24d authored over 9 years ago by Guangchuang Yu <[email protected]>
revert to previous version for compatible with CRAN version of ggplot2

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107950 bc3139a8-6...

45bd540dc0c5fe45d27a0e0dc634e4ecbd6d1313 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
update according to recent changes of ggplot2

50a40221765f130d442c4c430360d53dc8ac9835 authored over 9 years ago by GuangchuangYu <[email protected]>
update according to changes of ggplot2

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107869 bc3139a8-6...

14435e7909183f3839565e89cdae4b1bf9e95513 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
update according to changes of ggplot2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107869 b...

1d4d69144a07be8e15166f52f4285ec1bee20b02 authored over 9 years ago by Guangchuang Yu <[email protected]>
update rm.singleton.newick

e2fa961764b96c46b82e6422ed90c1662727d48f authored over 9 years ago by GuangchuangYu <[email protected]>
update rm.singleton.newick

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107840 b...

7182a17d291365c56772f61fedf4644fdaab62f2 authored over 9 years ago by Guangchuang Yu <[email protected]>
update rm.singleton.newick

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107840 bc3139a8-6...

a4a65b05e06d3c3f3bf5061d424a568b5bb4b278 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
bug fixed in gheatmap

c176bde6d578a02ca395f6748104e15be633a6d2 authored over 9 years ago by GuangchuangYu <[email protected]>
bug fixed in gheatmap

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107839 bc3139a8-6...

15aa47832cea34febe848403e5ecd35ef33c4b39 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
bug fixed in gheatmap

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107839 b...

6435900982680d2cd57ffe7cc364b00f94f5b21f authored over 9 years ago by Guangchuang Yu <[email protected]>
subview function

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107837 bc3139a8-6...

6cb61e1dccd3b571b9b99e31460a182eb7dc08ee authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
subview function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107837 b...

2ab2876d5e92454869c3307ea6f3c8e2656630ef authored over 9 years ago by Guangchuang Yu <[email protected]>
subview

e2feb7ad0e9f89f4a913a5211fa2bfabb6a3743f authored over 9 years ago by GuangchuangYu <[email protected]>
update readme

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107527 b...

602aa799f78c24aa41382f10a6d274c60f8ea9ea authored over 9 years ago by Guangchuang Yu <[email protected]>
update readme

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107527 bc3139a8-6...

b3eb23cd1963906f62f93f99c9b7cde6494eab1a authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
update readme

5dbebef6fe6f0dbdc8f5bf8e464ea964ef91942a authored over 9 years ago by GuangchuangYu <[email protected]>
update readme

443f59459fe56dbcbd3fc855df814a8ba37c8f52 authored over 9 years ago by GuangchuangYu <[email protected]>
add citation in readme

bd9116e164a7521fb1422d174fb069f7a4dbd3ed authored over 9 years ago by GuangchuangYu <[email protected]>
add citation in readme

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107526 bc3139a8-6...

60b585ee4b9da2b9f18ed6649258439a28804b77 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
add citation in readme

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107526 b...

db5af712ad870a06b6a9ba68624ef17ede209b3d authored over 9 years ago by Guangchuang Yu <[email protected]>
fixed typo

c4b6756f5876db50555880331d1eb64792d2e817 authored over 9 years ago by GuangchuangYu <[email protected]>
fixed typo

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107497 b...

5144334935d7c714dcb3541d302e801e4122853e authored over 9 years ago by Guangchuang Yu <[email protected]>
fixed typo

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107497 bc3139a8-6...

744e70686a97162140eda3b70c110890c5783d2b authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
update citation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107495 bc3139a8-6...

ac941d57219b8f0660eb66bc2ec28e3aea4dcb86 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
update citation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107495 b...

8d0a47fbe64e8e416e676aff745d5430db4c2bbf authored over 9 years ago by Guangchuang Yu <[email protected]>
update citation

05eea433fa8dce6634e04ee8bee6fd992f61c0e7 authored over 9 years ago by GuangchuangYu <[email protected]>
import gpar

1a84d94709f4102d3ffc069c48179f85b7b5c18b authored over 9 years ago by GuangchuangYu <[email protected]>
import gpar

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107376 b...

237dfed4f30ebcb24c0ba01ad796c1fb00f0916e authored over 9 years ago by Guangchuang Yu <[email protected]>
import gpar

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107376 bc3139a8-6...

69abebbd9cf091d7e4e0473cd3cff58bd0dea478 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
update add_legend

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107375 b...

b73d586d9cf0fbce83a2a87f1f91c24fa78bf500 authored over 9 years ago by Guangchuang Yu <[email protected]>
update add_legend

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107375 bc3139a8-6...

631b5f8e01d7fa9c663cd49c0073085a4dea9094 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
update add_legend

1302c15a830eda5f33d329ee3c3b9e3a07871500 authored over 9 years ago by GuangchuangYu <[email protected]>
reroot method

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107219 bc3139a8-6...

8a63a407b40fb20e0af1cdd7a0a21114acf763e0 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
reroot method

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107219 b...

6e4f67da48c023090d10f9a8bdf26ee7aa15ddfa authored over 9 years ago by Guangchuang Yu <[email protected]>
reroot method

0932d4a5bfbf3c3937bbee3874515f824cc7c475 authored over 9 years ago by GuangchuangYu <[email protected]>
update paml_rst to compatible with only marginal ancestral sequence or joint ancestral sequence available

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107217 bc3139a8-6...

0e6f29a74ea6ac1e972dc1eca91a8ce6768cdc3e authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
update paml_rst to compatible with only marginal ancestral sequence or joint ancestral sequence available

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107217 b...

b8403a578c4740b57190556bce11aca01d43fe43 authored over 9 years ago by Guangchuang Yu <[email protected]>
update paml_rst to compatible with only marginal ancestral sequence or joint ancestral sequence available

e9c834bb57a4e3b11c61abec7fc7a4a0e60d55ba authored over 9 years ago by GuangchuangYu <[email protected]>
add doc

dfd32e25a82b27e27f859d793f676982852d7c49 authored over 9 years ago by GuangchuangYu <[email protected]>
add doc

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106970 bc3139a8-6...

34a4198c21030d9d65f265cc3f1365a5caf04fa4 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
add doc

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106970 b...

bedbd8941e8172e4d7cce775893a61a9683fe76d authored over 9 years ago by Guangchuang Yu <[email protected]>
annotation_image

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106969 bc3139a8-6...

bc33be173215a18b9db803bc3f9a79662e06e3b4 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
annotation_image

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106969 b...

5cfb0ffa5ad5ba95c365942392ed1636418544a7 authored over 9 years ago by Guangchuang Yu <[email protected]>
annotation_image

dbb2f7596d2fda5d05d9099647e95227d8130d88 authored over 9 years ago by GuangchuangYu <[email protected]>
add external doc

9c00f8dd9733e31b915f17ef7d58a1034db3fe68 authored over 9 years ago by GuangchuangYu <[email protected]>
add external doc

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106966 bc3139a8-6...

a0025f2a5add86d69ba17fbb39cb9571a0c02ee8 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
add external doc

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106966 b...

e305d82710b5908042523797267b09c72327aaf8 authored over 9 years ago by Guangchuang Yu <[email protected]>
group_name parameter of groupOTU/groupClade and new geom_tiplab

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106964 bc3139a8-6...

8d2e3b032725bd7549b9eb2d43f494752535b830 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
group_name parameter of groupOTU/groupClade and new geom_tiplab

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106964 b...

68c7ac990edcd0ca5ac7f8601d2a5c77692f4fdb authored over 9 years ago by Guangchuang Yu <[email protected]>
group_name parameter of groupOTU/groupClade and new geom_tiplab

fad68f3c3078fd0c21c0466b81515917c1ba7227 authored over 9 years ago by GuangchuangYu <[email protected]>
update vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106948 b...

b529fdd76e8edf6596206238a341d374cd444c4b authored over 9 years ago by Guangchuang Yu <[email protected]>
update vignette

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106948 bc3139a8-6...

12632f96d6b14aef8afd7edfa2bb8ce28cedbbd0 authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
update vignett

33c70d36dbdd5c633011fd4bfc8ea53bf71e5a19 authored over 9 years ago by GuangchuangYu <[email protected]>
better geom_tree/groupClade/groupOTU implementation & annotation_clade/annotation_clade2 functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106946 b...

94bf49f9c35179487d4b00ba4b10e96e45b31659 authored over 9 years ago by Guangchuang Yu <[email protected]>
better geom_tree/groupClade/groupOTU implementation & annotation_clade/annotation_clade2 functions

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106946 bc3139a8-6...

291e937020907cc5957354e36736fcd197ac2fca authored over 9 years ago by g.yu <g.yu@bc3139a8-67e5-0310-9ffc-ced21a209358>
update vignette

98416f3d4b2550e245a8f681a22b11ed4fbb2dc0 authored over 9 years ago by GuangchuangYu <[email protected]>
groupClade for tree view and mapping parameter in ggtree

9ceb54d641ddaf7d4279b78ae8d5a820c229a7fa authored over 9 years ago by GuangchuangYu <[email protected]>
extend groupOTU to support operating on tree view <2015-07-31, Fri>

da8a6294ee273bd5a514eb10900365728629f9fd authored over 9 years ago by GuangchuangYu <[email protected]>
svn-git coexist

b15351b7c223c03d26168db33a48af9a47cede68 authored over 9 years ago by GuangchuangYu <[email protected]>
groupOTU & groupClade

6b0e251eb475162aa9a2a22e70ff4a275e74e5ab authored over 9 years ago by GuangchuangYu <[email protected]>
annotation_clade and annotation_clade2

7f3ddc15a0caf7bd55b5ae61a87e248b423f016b authored over 9 years ago by GuangchuangYu <[email protected]>