Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / emmanuelparadis/pegas issues and pull requests

#90 - Ops.factor(left, right) error

Issue - State: open - Opened by SimeoneCA 5 months ago

#89 - Subset a haplotype object based on names?

Issue - State: open - Opened by ChrisK1988 6 months ago - 2 comments

#88 - Issue with replot() on Windows

Issue - State: closed - Opened by Chatchamew 7 months ago - 2 comments

#87 - Duplicated Sequence for MJN

Issue - State: open - Opened by Chatchamew 7 months ago - 11 comments

#86 - default number of iterations in rmst() might not be enough

Issue - State: closed - Opened by emmanuelparadis 8 months ago - 1 comment
Labels: enhancement

#85 - rmst on a list of distance matrices

Issue - State: closed - Opened by naurasd 8 months ago - 6 comments

#84 - Introduce threshold parameter for show.mutation

Issue - State: open - Opened by naurasd 12 months ago
Labels: enhancement

#83 - Changing node coordinates changes node scale

Issue - State: closed - Opened by naurasd about 1 year ago - 2 comments

#82 - Positioning of haplotypes in network different everytime the plot is re-done

Issue - State: closed - Opened by naurasd about 1 year ago - 6 comments

#81 - Alternative links - placement of mutation ticks

Issue - State: closed - Opened by naurasd about 1 year ago - 7 comments

#80 - Plotting labels next to haplotypes, not onto them

Issue - State: closed - Opened by naurasd about 1 year ago - 3 comments

#79 - Error Reading In Fasta Data

Issue - State: closed - Opened by sbabbbie about 1 year ago - 1 comment

#78 - [pegas 1.2] Median Joining network with wrong number of mutations ?

Issue - State: closed - Opened by ColineRoyaux about 1 year ago - 2 comments

#77 - possible error in tajima.test that causes miscalculation of the statistic

Issue - State: closed - Opened by omys-omics over 1 year ago - 2 comments
Labels: bug

#76 - Creating Median Joining Networks

Issue - State: closed - Opened by leshonlee over 1 year ago - 3 comments
Labels: question

#75 - How to get the same result as DnaSp in haplotype extraction?

Issue - State: closed - Opened by jaum20 almost 2 years ago - 10 comments

#74 - Problems with replot function

Issue - State: closed - Opened by Juanphg about 2 years ago - 2 comments

#73 - Color the pies of haplonet

Issue - State: closed - Opened by QianGuoPKU about 2 years ago - 4 comments

#72 - The network algorithm in Haplonet function

Issue - State: closed - Opened by QianGuoPKU over 2 years ago - 2 comments

#71 - Two haplotypes are plotted with the same colour if bg is specified

Issue - State: closed - Opened by vmkalbskopf over 2 years ago - 11 comments

#70 - Known haplotype frequencies

Issue - State: closed - Opened by Timzladen over 2 years ago - 1 comment

#69 - Results from MMD Function

Issue - State: closed - Opened by S-Majoros over 2 years ago - 2 comments

#67 - Computing the frequencies of haplotypes for each population from "loci" objects

Issue - State: closed - Opened by awshort over 2 years ago - 2 comments

#66 - Extracting the frequencies from a "haplotype.loci" object

Issue - State: closed - Opened by awshort over 2 years ago - 2 comments

#65 - Adding the pairwise deletion argument to the dist.asd () function

Issue - State: closed - Opened by DenisGoryunov over 2 years ago - 3 comments

#64 - Updated vcf conflicts with cache

Issue - State: closed - Opened by jnrunge almost 3 years ago - 2 comments

#63 - Problem ploting haplonet with mutations as dots (show.mutation=2)

Issue - State: closed - Opened by Juanphg almost 3 years ago - 2 comments

#62 - Make adegenet a Suggests package?

Issue - State: closed - Opened by privefl almost 3 years ago - 3 comments

#61 - Issue with identifying haplotypes

Issue - State: closed - Opened by mkiravn about 3 years ago - 2 comments

#60 - error with reading two rows per individual in "haplotype"

Issue - State: closed - Opened by aherbotany about 3 years ago - 9 comments

#58 - Issue with reading in VCF files

Issue - State: closed - Opened by mkiravn over 3 years ago - 15 comments

#57 - Warning issued by amova within pegas

Issue - State: closed - Opened by green-striped-gecko over 3 years ago - 3 comments

#55 - Current haplotype.r version won't plot other pie colors

Issue - State: closed - Opened by cajwalsh over 3 years ago - 6 comments

#54 - Add your repository to r-universe.dev?

Issue - State: closed - Opened by zkamvar over 3 years ago

#53 - Running haplotype() on an empty dna object

Issue - State: closed - Opened by kweitemier over 3 years ago - 2 comments

#52 - Fst now runs in case of single population (fixes #51)

Pull Request - State: closed - Opened by courtiol over 3 years ago - 1 comment

#51 - Fst() does not run in case of a single population

Issue - State: closed - Opened by courtiol over 3 years ago

#50 - LD2 fails

Issue - State: closed - Opened by stuartwillis about 4 years ago - 3 comments

#49 - Bug in FST calculation

Issue - State: closed - Opened by Ahhgust about 4 years ago - 2 comments

#48 - Fixing node scale across pegas haplotype network plots

Issue - State: closed - Opened by ksw9 about 4 years ago - 5 comments

#47 - Testing HWE for X-chromosomal markers

Issue - State: open - Opened by cloudred20 over 4 years ago - 1 comment
Labels: enhancement

#46 - Get differences between haplotypes

Issue - State: closed - Opened by jcgrenier over 4 years ago - 4 comments

#45 - Missing data Handling

Issue - State: closed - Opened by jcgrenier over 4 years ago - 2 comments

#44 - Problems with LDScan

Issue - State: closed - Opened by nschan almost 5 years ago - 6 comments

#43 - Haplotype mutation ticks in center of links

Issue - State: closed - Opened by mhoban about 5 years ago - 4 comments

#42 - MMD documentation typo help?

Issue - State: closed - Opened by aeberardi over 5 years ago - 1 comment

#41 - drop = FALSE in ".[loci"creates issues with other function(s)

Issue - State: closed - Opened by courtiol over 5 years ago - 1 comment

#40 - read.loci() silently deleting samples on import

Issue - State: closed - Opened by emmanuelparadis over 5 years ago - 5 comments

#39 - some functions not installed

Issue - State: closed - Opened by willyard almost 6 years ago - 1 comment

#38 - All NaN from Fst function

Issue - State: closed - Opened by darencard about 6 years ago - 2 comments

#37 - Fix loci subset method dispatch

Pull Request - State: closed - Opened by zkamvar about 6 years ago - 1 comment

#36 - hw.test fails if a locus contains all missing data

Issue - State: closed - Opened by zkamvar about 6 years ago - 8 comments

#35 - crash - address (nil), cause 'memory not mapped' on opensuse tumbleweed

Issue - State: closed - Opened by zjons over 6 years ago - 1 comment

#34 - created write.amova

Pull Request - State: closed - Opened by knausb over 6 years ago - 3 comments

#33 - First P value missing for hierarchical AMOVA with 2 or more tiers [new]

Issue - State: closed - Opened by ghost over 6 years ago - 2 comments

#32 - Plot opens graphics output but never plots anything, just sits there

Issue - State: closed - Opened by DiDeoxy over 6 years ago - 1 comment

#31 - Add new function getPhi()

Pull Request - State: closed - Opened by zkamvar over 6 years ago - 1 comment

#30 - problem with SNP without polymorphism from VCF

Issue - State: closed - Opened by frederic-michaud over 6 years ago - 6 comments

#29 - Expanding the file name of vcf file to be read to avoid segfault.

Pull Request - State: closed - Opened by frederic-michaud over 6 years ago - 1 comment

#28 - Session crash when loading vcf file with ~

Issue - State: closed - Opened by frederic-michaud over 6 years ago - 2 comments

#27 - add missing comma

Pull Request - State: closed - Opened by zkamvar over 6 years ago - 2 comments

#26 - fix levels for print.amova

Pull Request - State: closed - Opened by zkamvar almost 7 years ago - 2 comments

#25 - Feature request: Calculate phi statistics for AMOVA

Issue - State: closed - Opened by zkamvar almost 7 years ago - 5 comments

#24 - pop function exported in hw.test?

Issue - State: closed - Opened by EricArcher almost 7 years ago - 5 comments

#23 - unexpected behavior when trying to install pegas with githubinstall()

Issue - State: closed - Opened by vinsondoyle over 7 years ago - 3 comments

#22 - Error when using haploNet(h) on Fasta file.

Issue - State: closed - Opened by jorgeamaya over 7 years ago - 1 comment

#21 - loci2genind and ploidy level?

Issue - State: closed - Opened by jgx65 about 8 years ago - 3 comments

#20 - Problem with missing values in loci2genind

Issue - State: closed - Opened by mstetter about 8 years ago - 3 comments

#19 - Absent sigma/p value with multi-level amova plus warnings

Issue - State: closed - Opened by elizeng over 8 years ago - 1 comment

#18 - P values absent in some AMOVA runs with hierarchical levels

Issue - State: closed - Opened by CEMoffat over 8 years ago - 2 comments

#17 - error message with theta.msat

Issue - State: closed - Opened by kathfi over 8 years ago - 1 comment

#16 - error message with theta.msat

Issue - State: closed - Opened by kathfi over 8 years ago - 5 comments

#15 - fixing conversion from loci to genind - . treated as NA

Pull Request - State: closed - Opened by thibautjombart almost 9 years ago - 1 comment

#14 - NAs in loci2genind "." treated as an allele

Issue - State: closed - Opened by thibautjombart almost 9 years ago - 1 comment

#13 - when would hw.test produce NA?

Issue - State: closed - Opened by romunov almost 9 years ago - 1 comment

#12 - conversion issue genind objects

Issue - State: closed - Opened by juance100 about 9 years ago - 1 comment

#11 - enhancement for read.vcf function?

Issue - State: closed - Opened by lduvaux about 9 years ago - 1 comment

#10 - Potential bug / conversion issue

Issue - State: closed - Opened by thibautjombart about 9 years ago - 3 comments

#9 - as.romans not found in utils

Issue - State: closed - Opened by zkamvar about 9 years ago - 1 comment

#8 - Change util to utils in imports

Pull Request - State: closed - Opened by zkamvar over 9 years ago - 1 comment

#7 - The link to fstat in pegas Fst help is no longer valid

Issue - State: closed - Opened by thibautjombart over 9 years ago - 6 comments

#6 - hw.test.R problem with data set ncol > 170

Issue - State: closed - Opened by thierrygosselin over 9 years ago - 2 comments

#5 - filter out haplotypes by frequency

Issue - State: closed - Opened by emmanuelparadis over 9 years ago - 5 comments

#4 - haplotype network from the "haplotype.loci" class

Issue - State: closed - Opened by emmanuelparadis over 9 years ago - 6 comments

#3 - haploNet

Issue - State: closed - Opened by jhmarcus over 9 years ago - 4 comments

#2 - Fix rhs/data issue in amova

Pull Request - State: closed - Opened by zkamvar over 9 years ago - 5 comments

#1 - Implementation of hw.test as generic + methods

Pull Request - State: closed - Opened by thibautjombart over 9 years ago - 3 comments