Tag: Nexus

Integrative analysis of eQTL and GWAS summary statistics reveals transcriptomic alteration in Alzheimer brains | BMC Medical Genomics

Significant gene-AD associations With the GWAS summary data from the IGAP and eQTL summary data from BRAINEAC, we performed both SMR and HEIDI tests to estimate the gene-AD associations in three human brain regions: frontal cortex, temporal cortex, and hippocampal regions. For the frontal cortex and hippocampal regions, we obtained…

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phylogenetics – Biopython reads my tree eternally long

I have a nexus tree (1332 taxa) with a lot of additional data. When I tried to read it through tree = Phylo.read(treepath, “nexus”), my kernel got eternally loaded. If I abort the process, I get the following message: ————————————————————————— KeyboardInterrupt Traceback (most recent call last) Input In [95], in…

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Postdoctoral Scientist – Knott Lab

Details Posted: 09-Apr-22 Location: Los Angeles, California Type: Full-time Salary: Open Categories: Staff/Administrative Internal Number: HRC0544032D Principal Investigator, Simon Knott, PhD is looking for a Postdoctoral Scientist to join the team! The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group with the common goal…

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Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

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H2O is an in-memory platform for distributed, scalable machine learning

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

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Fasta file reading python

Answer by Aidan Golden I think you can just use Biopython,It is indeed wrong today. I edited the answer since it has been possible to use str(sequence) for a long time now.,Very useful answer from 7 years ago! FYI, in current version of biopython(1.69), fasta.seq.tostring() is obsolete, use str(fasta.seq) instead.,Nicely…

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Postdoctoral Scientist – Knott Lab – Bioinformatics & Functional Genomics

Requisition # HRC0544032C Principal Investigator, Simon Knott, PhD is looking for a Postdoctoral Scientist to join the team! The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient…

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