The bioinformatics chat is a podcast about computational biology, bioinformatics, and next generation sequencing.
The bioinformatics chat is produced by Roman Cheplyaka.
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May 31, 2018
Linear mixed models are used to analyze GWAS data and detect QTLs.
Andrey Ziyatdinov recently released an R package, lme4qtl, that can be used to
formulate and fit these models.
In this episode Andrey and I discuss linear mixed models, genome-wide association studies, and strengths and weaknesses of lme4qtl.
April 30, 2018
In this episode
present their project called SPURF.
SPURF can predict the B cell receptor (BCR) substitution profile of a given clonal
family based on a single representative sequence from that family.
SPURF works by fitting a tensor regression model to publicly available
April 7, 2018
In this episode Gustavo Glusman explains his method of reducing a VCF file
to a small “fingerprint”, which could be then used to detect duplicate genomes,
infer relatedness, map the population structure, and more.
#18 Bioinformatics Contest 2018 with Alexey Sergushichev and Ekaterina Vyahhi
#17 Rarefaction, alpha diversity, and statistics with Amy Willis
#16 Javier Quilez on what makes large sequencing projects successful
#15 Optimal transport for single-cell expression data with Geoffrey Schiebinger
#14 Generating functions for read mapping with Guillaume Filion
#13 Bracken with Jennifer Lu
#12 Modelling the immune system and C-ImmSim with Filippo Castiglione
#11 Collective cell migration with Linus Schumacher
#10 Spatially variable genes and SpatialDE with Valentine Svensson
#9 Michael Tessler and Christopher Mason on 16S amplicon vs shotgun sequencing
#8 Perfect k-mer hashing in Sailfish
#7 Metagenomics and Kraken
#6 Allele-specific expression
#5 Relative data analysis and propr with Thom Quinn
#4 ChIP-seq and GenoGAM with Georg Stricker and Julien Gagneur
#3 miRNA target site prediction and seedVicious with Antonio Marco
#2 Single-cell RNA sequencing with Aleksandra Kolodziejczyk
#1 Transcriptome assembly and Scallop with Mingfu Shao