Tag: PopGen

PCA from plink2 for SGDP using a pangenome and DeepVariant

Hi there, I’m doing my first experiments with PCA and UMAP as dimensionality reductions to visualize a dataset I’ve been working on. Basically, I used the samples from the SGDP which I then mapped on the human pangenome for, finally, calling small variants with DeepVariant. I moved on with some…

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Disease signatures in the gut metagenome of a prospective family cohort of inflammatory bowel disease

Abstract Inflammatory bowel disease (IBD) is associated with dysbiotic microbiomes. However, whether microbiomes of family members of IBD patients harbour microbial disease signatures of IBD is unknown. Here, we generate shotgun metagenomic data of an IBD family cohort and treatment-naive IBD cases, which we combine with published IBD metagenomes, to…

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Postdoctoral Fellowship in bioinformatics and genetic epidemiology – University of Copenhagen – job portal

Job Portal                                                                                         Postdoctoral Fellowship in bioinformatics and genetic epidemiology   A two-year postdoctoral fellowship is available at the Section for Computational and RNA Biology, Department of Biology, University of Copenhagen. The position will be available from April 1st, 2024 or thereafter. The specific projects involve analyzing…

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Head of the Medical Bioinformatics platform (m/f/d) – Kiel

Das Universitätsklinikum Schleswig-Holstein (UKSH) verbindet internationale Spitzenforschung mit interdisziplinärer Krankenversorgung. Wir sind einziger Maximalversorger und größter Arbeitgeber des Landes. Unsere mehr als 14.500 Mitarbeiter*innen stellen eine höchst individuelle Versorgung sicher – unverzichtbar für die Menschen in Schleswig-Holstein.The Institute of Clinical Molecular Biology (IKMB)The Medical Faculty together with the Institute of…

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Bioinformatics Programming with Biopython: Advanced Biopython Techniques for Computational Biology | by Bao Tram Duong | Nov, 2023

Biopython is an open-source collection of Python tools for computational biology and bioinformatics. It provides modules and classes to work with biological data such as DNA, RNA, protein sequences, structures, and more. Biopython aims to make it easy for developers to access and manipulate biological data in a programmatic way….

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GenAlEx Haploid Data Detecting Recombination

GenAlEx Haploid Data Detecting Recombination 0 Hello, I am currently using GenAlEx to try and detect if recombination is present in both of my populations. My data consists of 4 Loci with one allele per locus. GenAlEx seems to have options for Paired biallelic LD, but I am struggling with…

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Postdoc position (m/f/d) Intestinal metablomics in health and disease

Stellenbeschreibung Das Universitätsklinikum Schleswig-Holstein (UKSH) verbindet internationale Spitzenforschung mit interdisziplinärer Krankenversorgung. Wir sind einziger Maximalversorger und größter Arbeitgeber des Landes. Unsere mehr als 14.500 Mitarbeiter*innen stellen eine höchst individuelle Versorgung sicher – unverzichtbar für die Menschen in Schleswig-Holstein. The Institute of Clinical Molecular Biology (IKMB) offers 1 position for a…

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Detecting introgressive hybridization to maintain genetic integrity in endangered large waterbird: a case study in milky stork

Rhymer, J. M. & Simberloff, D. Extinction by hybridization and introgression. Annu. Rev. Ecol. Evol. Syst. 27, 83–109 (1996). Article  Google Scholar  Dowling, T. E. & Secor, C. L. The role of hybridization and introgression in the diversification of animals. Annu. Rev. Ecol. Evol. Syst. 28, 593–619 (1997). Article  Google…

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where to find the ANOVA?

I repeatedly read that LIMMA is performing an ANOVA analysis, apparently always in the background, and also that the ANOVA results are obtainable. Unfortunately, though, I can’t get/find this information and would appreciate it a lot if someone could enlighten me. Below, I post the code I use to get…

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Calculate the kinship matrix from NGS data

I wish to calculate the kinship matrix from a batch of Next Generation Sequencing (NGS) data. Previously, I have tried to use PCAngsd 0.98 to output the matrix, but it seems that this option does not exist any more since the previous version of the software PCAngsdv2. www.popgen.dk/software/index.php/PCAngsd www.popgen.dk/software/index.php/PCAngsdv2 Would…

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Ubuntu Manpage: Bio::PopGen::IO::phase – A parser for Phase format data

Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::PopGen::IO::phase – A parser for Phase format data SYNOPSIS # Do not use directly, use through the Bio::PopGen::IO driver use Bio::PopGen::IO; my $io = Bio::PopGen::IO->new(-format => ‘phase’, -file => ‘data.phase’); # Some IO might support reading in a population at a time my @population; while( my…

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Virtual RAD-seq Analysis Workshop!

News:Virtual RAD-seq Analysis Workshop! 0 The Computational Biology Core at the University of Connecticut’s Institute for Systems Genomics is offering a virtual RAD-seq analysis workshop April 17-20 2023. The workshop will cover an introduction to linux and high performance computing before going through a complete analysis starting with raw reads…

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Shining a light on dark genes

 Countries around the world have recognized the value of precision health and population genomics research initiatives. They have launched efforts to sequence thousands to millions of genomes in order to learn more about how complex or rare inherited diseases impact their populations and how to mitigate their impacts. The goal?…

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Ubuntu Manpage: Bio::PopGen::IO::prettybase – Extract individual allele data from PrettyBase format

Provided by: libbio-perl-perl_1.7.2-3_all NAME Bio::PopGen::IO::prettybase – Extract individual allele data from PrettyBase format SYNOPSIS Do not use directly, use through the Bio::PopGen::IO driver DESCRIPTION This object will parse comma delimited PrettyBase output. PrettyBase is defined by the SeattleSNPs pga.gs.washington.edu/ This is expected to be tab delimited (you can vary with…

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Difference between python and biopython

Biopython vs Python Hi, Please help – If already have python 3 in laptop, is biopython still needed to download? I already downloaded python 3; when I checked on the www.bippython.org, there is also “download”, are they the same or different? sorry if it is a naive question. Thank you…

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Test DSSP generation from MMCIF with non-standard residues.

Hi Maarten, This seems to stem from your latest upload of dssp. Could you consider taking a look at this one? Thanks, Nilesh On Sun, 1 Jan 2023 15:20:12 +0100 Lucas Nussbaum <lu…@debian.org> wrote: > Source: python-biopython > Version: 1.80+dfsg-4 > Severity: serious > Justification: FTBFS > Tags: bookworm sid ftbfs > User: lu…@debian.org > Usertags: ftbfs-20230101 ftbfs-bookworm > >…

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Index of /~birch/birchhomedir/dat/dGDE/GDEHELP-osx-x86_64/doc/mesquite/doc/popGen/images

Name Last modified Size Description Parent Directory   –   assoc.gif 2003-08-26 14:07 18K   assoc2.gif 2003-08-26 14:07 6.2K   assocEst.gif 2003-08-26 14:07 18K   assocList.gif 2003-08-26 14:07 11K   createNewPop.gif 2003-08-26 14:08 24K   depths.gif 2003-08-26 14:08 6.2K   depths10000.gif 2003-08-26 14:08 7.2K   geneTree.gif 2003-08-26 14:08 3.2K  …

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Population genomics using ancient DNA data

News:Population genomics using ancient DNA data 0 Dear all, registrations are now open for the ONLINE Physalia course on “Population genomics using ancient DNA data” Dates: 31 January- 4 February Course website: www.physalia-courses.org/courses-workshops/adna-popgen/ Instructors: Dr C. Eduardo Guerra Amorim (California State University Northridge, USA) and Diana Cruz-Davalos (University of Lausanne,…

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