pegas Posts

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198

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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 5 months ago by mariaemilyd • 0 • updated 4 months ago by _r_am ♦ 32k

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504

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haplotype network analysis with Pegas package in R

R pegas haplotype written 8 months ago by Ana • 180

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294

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

R pegas alignment population genetics written 16 months ago by juliuspasion1994 • 10

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1.4k

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Formatting Haplotype Network in R

R pegas haplotypenetwork written 2.1 years ago by christinafragel • 0 • updated 23 months ago by zx8754 ♦ 9.9k

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1.6k

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Identifying mutations between haplotypes using haploNet (pegas) in R

haplotypes R pegas phylogenetics written 2.8 years ago by GabrielMontenegro • 570 • updated 2.6 years ago by Jie Ping • 30

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3.2k

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Pegas import fasta and calculate theta

fasta R pegas theta written 6.0 years ago by Adrian Pelin • 2.4k • updated 6.0 years ago by David W ♦ 4.8k

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Recent Replies

A: What is the difference between Average Nucleotide Identity (ANI) and blastn anal by 5heikki ♦ 9.2k
Blastn is a tool for local nucleotide sequence alignments. ANI generally refers to average nucleo...
C: In methylation sequencing, what does BedGraph value stand for? by devarora • 270
Fourth column belongs to probability scores (Methylation value) for the given position at specifi...
A: CHIP-Seq data mapping using Bowtie2 by Qiongyi • 100
Low mapping ratio may be due to contaminations or poor quality of your sequencing libraries. You ...
A: Error in running RSEM by Qiongyi • 100
You should use "--bowtie2-path" rather than "--bowtie-path"
C: Extracting the Predicted Reults of Neural network in R by Jean-Karim Heriche ♦ 24k
This is not a bioinformatics question but an R programming one.
A: Calling triovariants using varscan from a compressed mileup file ? by svp • 410
You can try: `< zcat (file.gz)` as input varscan trio < (zcat trio.mileup.gz) trio.mpi...
C: Is anybody experiencing problems downloading from the SRA? by svp • 410
It looks like the data is available in link ftp://ftp.sra.ebi.ac.uk/vol1/run/SRR124/SRR12492134/ ...
A: sra-explorer : find SRA and FastQ download URLs in a couple of clicks by elenichri • 10
Very convenient tool, much needed! Thanks a lot!
C: Aliases for gene names from Entrez gene search by gsr9999 • 140
edirect is a nice tool
C: WGCNA negative values by reara • 20
Sorry just to clarify-these are post normalization values. Do i take it that WGCNA cannot handle ...
C: Running Mauve on circular genomes by rthapa • 40
Were you able to solve the issue?
A: Bioinformatics Engineer (6 months) in Clinical Bioinformatics, Curie Institute, by priya.bmg • 0
After six months will the contract be extended? Thanks