nclark-lab RERconverge issues

nclark-lab / RERconverge

Analysis of convergence between organismal traits and DNA/protein sequences

GNU General Public License v3.0

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issues

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foreground2TreeClades, getPermsBinary runs without error, no results are given for a long time

#101 vincentkaiheng opened 1 week ago
2
Incorrect pseudorooting detected - use fixPseudoroot() function to correct trait tree topology

#100 YanCheer opened 1 month ago
1
fastwilcoxGMTall with Goterms instead of pathways

#99 MaximePolicarpo opened 2 months ago
2
How to get the RERs of ancestral nodes?

#98 zhxh233 opened 3 months ago
3
question about getAllResiduals

#97 SWei2333 opened 4 months ago
0
How to conduct tests for Phylogenetic Permutations of Binary Phenotypes with two ancestral branches?

#96 YuantingGuo opened 4 months ago
0
A large number of Duplicate columns and NA columns after running getAllResiduals

#95 huziouziou closed 5 months ago
1
can i provide a neutral tree with branch length as RERconverge master tree

#94 shuifeng1988 opened 5 months ago
2
RERconverge Install Error (M2 Mac OS Ventura 13.6.7)

#93 divittorion closed 5 months ago
1
whether RERconverge has to be used for converge ?

#92 zhxh233 opened 6 months ago
2
mamRERw result is NA

#91 cjl200095 opened 7 months ago
6
Ask a stupid question, where can i find the scripts in the NoncodingRegionWorkflow file

#90 shuifeng1988 opened 7 months ago
2
How to optimize parameters based on my current results?

#89 zhxh233 opened 8 months ago
2
Number of input species and explanation of output

#88 zhxh233 closed 8 months ago
4
Made changes to FullWalkthrough docs

#87 nclark-lab closed 8 months ago
0
Discordant gene trees

#86 navyashukla-uom closed 9 months ago
0
Add directionality to foreground2Paths

#85 MichaelTene7 closed 8 months ago
0
add clade and transition to binary perms

#84 MichaelTene7 closed 10 months ago
0
not enough genes with all species present: master tree has no edge.lengths

#83 chun-he-316 opened 10 months ago
2
Trouble installing on Intel Core Mac

#82 jules424 opened 11 months ago
1
RER speedup

#81 csestili opened 1 year ago
0
Michael categorical updates; Update CategoricalPermulations vignette to include relaxation, update categoricalPermulations function to relxable versions

#80 MichaelTene7 opened 1 year ago
0
Trouble installing RERconverge on M1 mac

#79 RishiDeKayne opened 1 year ago
3
Unable to load RERconverge on M1 Mac

#78 MattChristmas opened 1 year ago
2
Error when trying to read in treefile

#77 johnathanlo closed 1 year ago
8
Error: Mat::elem(): index out of bounds

#76 drabe004 opened 1 year ago
2
binarize option not working correctly in the tree2Paths function

#75 MichaelTene7 opened 1 year ago
1
Differences between clade-based correlation and non-clade based correlations?

#74 MichaelTene7 opened 1 year ago
1
Bioconda package

#73 jayramr closed 1 year ago
1
Update getPermsBinary with earlier non-numeric check

#72 MichaelTene7 opened 2 years ago
2
Permulations using `tree2Paths()`?

#71 micahpf opened 2 years ago
2
Different rho and p-values for the same gene in the table and figure

#70 pkfsantos closed 2 years ago
6
'masterTree' not found in SSM permulations

#69 ekopania closed 2 years ago
0
Error when running getAllResiduals (incorrect pseudorooting)

#68 laristide opened 2 years ago
2
Cannot Install RERconverge

#67 amgraham07 closed 2 years ago
7
Erro when using estimatePhangornTreeAll

#66 ZhangXu-CAS opened 2 years ago
5
long branch length due to missing

#65 LipengKang closed 2 years ago
3
Can RERconverge handle gene trees with duplicates?

#64 ghost opened 3 years ago
2
Labels in RERplots

#63 kjf319 opened 3 years ago
0
Pseudorooting of Genetrees

#62 kjf319 opened 3 years ago
0
Trouble calculating RER by getAllResiduals, all NA generated

#61 Frank1219 opened 3 years ago
11
Unable to Install Program

#60 andypaige772 opened 3 years ago
13
tree discordance and multiple-copy genes

#59 xiaoyezao opened 3 years ago
9
readTrees() and subsequent getAllResiduals errors

#58 1221li opened 3 years ago
3
Corrections made to Walkthrough

#57 nclark-lab closed 4 years ago
0
Output of fastwilcoxGMTAll

#56 evolgen closed 4 years ago
1
Issues installing RERconverge on R 4.0 (Mac OS Catalina 10.15.5)

#55 kjf319 closed 3 years ago
4
Gene tree input other than PAML

#54 evolgen closed 4 years ago
5
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent

#53 mbarkdull closed 4 years ago
11
Issues installing from binary on MacOS Mojave 10.14.6

#52 mbarkdull closed 4 years ago
6