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Issue converting 2 column allele data to 1 column using pegas::alleles2loci or genetics::makeGenotypes: switches order of alleles

R pegas makegenotypes alleles2loci microsatellite written 9 days ago by mariaemilyd • 0

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148

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haplotype network analysis with Pegas package in R

R pegas haplotype written 3 months ago by Ana • 170

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234

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How to prep MAFFT alignment files for use in R packages ape and pegas?

R pegas alignment population genetics written 11 months ago by juliuspasion1994 • 10

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1.1k

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Formatting Haplotype Network in R

R pegas haplotypenetwork written 20 months ago by christinafragel • 0 • updated 18 months ago by zx8754 ♦ 9.4k

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1.4k

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Identifying mutations between haplotypes using haploNet (pegas) in R

haplotypes R pegas phylogenetics written 2.4 years ago by GabrielMontenegro • 560 • updated 2.1 years ago by Jie Ping • 30

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3.0k

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Pegas import fasta and calculate theta

fasta R pegas theta written 5.6 years ago by Adrian Pelin • 2.4k • updated 5.6 years ago by David W ♦ 4.8k

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Recent Replies

C: Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vc by michaeldonaldson • 10
Hi Pierre, Can you clarify how the above script relates to allele balance (i.e., the proportion ...
C: nr database "No alias or index file found for protein database" by genomax ♦ 87k
With new default blast+ `v5` database, size of the files changed (individual files are now larger...
C: FastqToSam (Picard) syntax paired-end reads by h.mon ♦ 30k
Yes, but this splitting of files is uncommon nowadays. This was common when files were often tran...
C: EdgeR and contrasts: How to compare with a group not in the model by h.mon ♦ 30k
No, not when you set the intercept to zero. Even if the intercept isn't set to zero, one needs ...
A: ObjTables: tools for creating and reusing high-quality spreadsheets (e.g., suppl by jonrkarr • 60
Table Schema (Frictionless Data) is probably one of the closest general-purpose tools. Other simi...
C: Variant Quality Score Recalibration (Vqsr) For Non-Human Genomes by Begonia_pavonina • 20
Hello Jeremy, I had the same question than Tonyzeng and was wondering how I could filter my varia...
A: Publicly Available WGS Samples for Panel of Normals? by tjbencomo • 0
I ended up using the hg38 1000 Genomes PON from the Broad linked to by @RamRS. Although the PON w...
C: ObjTables: tools for creating and reusing high-quality spreadsheets (e.g., suppl by Jeremy Leipzig ♦ 19k
This looks super interesting. Can you compare ObjTables to Frictionless Data?
C: Query a public sql server from within python by genomax ♦ 87k
Can you do this as a subprocess/system call ([LINK][1])? [1]: https://stackoverflow.com/quest...
C: Adding gene set to GSVA by igor ♦ 11k
The problem is you are trying to convert it to a `GeneSetCollection` object. You don't need to do...
C: DE analysis with limma (What to include in the model?) by Davide • 10
I agree on the points Kevin is making. What are the DEG after using "adjusted p-values" for both ...
C: How to analyze Illumina RNASeq data by Manoj • 50
Hi, I am trying following command, however it is showing error. Please correct me, I am pretty ne...

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