emmanuelparadis pegas issues

emmanuelparadis / pegas

Population and Evolutionary Genetics Analysis System

GNU General Public License v2.0

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issues

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A dist.asd function warning with pairwise.deletion = TRUE parameter

#91 DenisGoryunov closed 1 month ago
3
Ops.factor(left, right) error

#90 SimeoneCA opened 3 months ago
3
Subset a haplotype object based on names?

#89 ChrisK1988 closed 1 month ago
2
Issue with replot() on Windows

#88 Chatchamew closed 4 months ago
2
Duplicated Sequence for MJN

#87 Chatchamew opened 4 months ago
11
default number of iterations in rmst() might not be enough

#86 emmanuelparadis closed 5 months ago
1
rmst on a list of distance matrices

#85 naurasd closed 6 months ago
6
Introduce threshold parameter for show.mutation

#84 naurasd opened 9 months ago
0
Changing node coordinates changes node scale

#83 naurasd closed 9 months ago
2
Positioning of haplotypes in network different everytime the plot is re-done

#82 naurasd closed 8 months ago
6
Alternative links - placement of mutation ticks

#81 naurasd closed 9 months ago
7
Plotting labels next to haplotypes, not onto them

#80 naurasd closed 10 months ago
3
Error Reading In Fasta Data

#79 sbabbbie closed 9 months ago
1
[pegas 1.2] Median Joining network with wrong number of mutations ?

#78 ColineRoyaux closed 1 year ago
2
possible error in tajima.test that causes miscalculation of the statistic

#77 omys-omics closed 1 year ago
2
Creating Median Joining Networks

#76 leshonlee closed 7 months ago
3
How to get the same result as DnaSp in haplotype extraction?

#75 jaum20 closed 1 year ago
10
Problems with replot function

#74 Juanphg closed 1 year ago
2
Color the pies of haplonet

#73 QianGuoPKU closed 2 years ago
4
The network algorithm in Haplonet function

#72 QianGuoPKU closed 2 years ago
2
Two haplotypes are plotted with the same colour if bg is specified

#71 vmkalbskopf closed 1 year ago
11
Known haplotype frequencies

#70 Timzladen closed 2 years ago
1
Results from MMD Function

#69 S-Majoros closed 2 years ago
2
Problem with the display of pie chart's colors with haplotype network median joining

#68 ColineRoyaux closed 2 years ago
6
Computing the frequencies of haplotypes for each population from "loci" objects

#67 awshort closed 2 years ago
2
Extracting the frequencies from a "haplotype.loci" object

#66 awshort closed 2 years ago
2
Adding the pairwise deletion argument to the dist.asd () function

#65 DenisGoryunov closed 2 years ago
3
Updated vcf conflicts with cache

#64 jnrunge closed 2 years ago
2
Problem ploting haplonet with mutations as dots (show.mutation=2)

#63 Juanphg closed 2 years ago
2
Make adegenet a Suggests package?

#62 privefl closed 2 years ago
3
Issue with identifying haplotypes

#61 mkiravn closed 2 years ago
2
error with reading two rows per individual in "haplotype"

#60 aherbotany closed 2 years ago
9
Error in .labelSegmentsHaploNet(xx, yy, altlink[s, 1:2, drop = FALSE], : argument "scale.ratio" is missing, with no default

#59 sheinasim closed 3 years ago
3
Issue with reading in VCF files

#58 mkiravn closed 3 years ago
15
Warning issued by amova within pegas

#57 green-striped-gecko closed 3 years ago
3
hw.test in pegas 1.0 and earlier failing many markers. EDIT: Markers were missing alleles present in pop.

#56 ptcooper closed 3 years ago
6
Current haplotype.r version won't plot other pie colors

#55 cajwalsh closed 3 years ago
6
Add your repository to r-universe.dev?

#54 zkamvar closed 2 years ago
0
Running haplotype() on an empty dna object

#53 kweitemier closed 3 years ago
2
Fst now runs in case of single population (fixes #51)

#52 courtiol closed 3 years ago
1
Fst() does not run in case of a single population

#51 courtiol closed 3 years ago
0
LD2 fails

#50 stuartwillis closed 3 years ago
3
Bug in FST calculation

#49 Ahhgust closed 3 years ago
2
Fixing node scale across pegas haplotype network plots

#48 ksw9 closed 4 years ago
5
Testing HWE for X-chromosomal markers

#47 cloudred20 opened 4 years ago
1
Get differences between haplotypes

#46 jcgrenier closed 4 years ago
4
Missing data Handling

#45 jcgrenier closed 4 years ago
2
Problems with LDScan

#44 nschan closed 4 years ago
6
Haplotype mutation ticks in center of links

#43 mhoban closed 3 years ago
4
MMD documentation typo help?

#42 aeberardi closed 5 years ago
1