Hlapers
Web16 gen 2024 · ALTHAPALIGNR and HLAPERS both align reads to a set of HLA haplotypes 22,23. The alignments are then used to infer haplotype-specific gene or transcript expression.
Hlapers
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Web1 gen 2024 · Europe PMC is an archive of life sciences journal literature. In Silico Typing of Classical and Non-classical HLA Alleles from Standard RNA-Seq Reads. Web6 giu 2024 · In this study, we quantified the allelic expression of all three HLA class I loci (HLA-A, B and C) by RNA sequencing and conducted an analysis of expression quantitative traits loci (eQTL) to investigate whether HLA expression regulation could be associated with non-coding gene variations. HLA-B alleles exhibited the highest expression levels ...
Web3 mar 2024 · HLApers can be employed for HLA typing and expression estimation directly from NGS data, thus contributing to understand how to increase success in predicting … WebHLApers: HLA Typing and Quantification of Expression with Personalized Index Vitor R. Aguiar et al., 2024, Springer Protocols AmpliSAS and AmpliHLA: Web Server Tools for MHC Typing of Non-Model Species and Human Using NGS Data
WebHowever, the increasing abundance of short-read sequencing data has prompted a demand for computational tools capable of HLA typing from general purpose sequencing data as well. OptiType is a software that performs HLA typing from short-read DNA and RNA sequencing data, and this chapter guides the user through its installation and usage. less. WebDownload scientific diagram Schematic representation of the HLApers pipeline to estimate HLA expression. The reads generated by RNA-seq are represented by curved shapes.
WebExpression was estimated with the HLApers pipeline. Horizontal lines inside each box represent the median. The lower and upper hinges correspond to the first and third quartiles respectively. The whisker lines extend from the hinges to the largest value no further than ±1.5 × IQR from the hinge (where IQR is the inter-quartile range, or distance between the …
Web28 gen 2024 · Additionally, we ran HLApers (Aguiar et al. 2024) and Kourami (Lee and Kingsford 2024) to infer HLA alleles directly from RNA-seq, and checked for agreement with the Sanger sequencing-based calls. If we consider consistent calls between HLApers and Kourami, we observed only 10 discordances with the Sanger calls out of 288 … in the gym hunterWebusing current commit, in a docker / conda environment ############## docker run --rm -v pwd:/data -w /data rna-hla-hlapers /bin/bash -c '/opt/conda run --no ... new horizon repositoryWeb22 dic 2012 · Because the algorithm uses standard RNA-Seq reads and requires no change to laboratory protocols, it can be used for both existing datasets and future studies, thus adding a new dimension for HLA typing and biomarker studies. We present a method, seq2HLA, for obtaining an individual's human leukocyte antigen (HLA) class I and II type … new horizon rentonWeb20 ore fa · CINCINNATI -- Taking ground balls at first base was not supposed to be part of Bryce Harper 's rehab from Tommy John surgery. But Harper was out early Thursday working with infield coach Bobby Dickerson. Phillies manager Rob Thomson was impressed with what he saw. "I didn't see him yesterday, but I was out there today," Thomson said. inthegymhoops showcaseWeb16 mar 2024 · HLApers License. HLApers integrates software such as kallisto, Salmon and STAR. Before using it, please read the license notices here. Getting started Install … new horizon research center miamiWeb28 set 2024 · The personalized pipeline of HLApers demonstrated several advantages such as higher accuracy in read alignment, HLA allele-specific expression quantification, and … new horizon release dateWeb1 giorno fa · Matt Gelb of the Athletic reports that Harper is preparing to work at first base. The primary benefit is that it may expedite his ability to take the field by reducing the … new horizon renovations salem oregon