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Meals & nutrition

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Hermann Romanov
Hermann Romanov

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KnowSeq KnowSeqproposes a whole pipeline that comprises the most relevant steps inthe RNA-seq gene expression analysis, with the main goal ofextracting biological knowledge from raw data (DifferentialExpressed Genes, Gene Ontology enrichment, pathway visualizationand related diseases). In this sense, KnowSeq allows aligning rawdata from the original fastq or sra files, by using the mostrenowned aligners such as tophat2, hisat2, salmon and kallisto.Nowadays, there is no package that only from the information of thesamples to align -included in a text file-, automatically performsthe download and alignment of all of the samples. Furthermore, thepackage includes functions to: calculate the gene expressionvalues; remove batch effect; calculate the Differentially ExpressedGenes (DEGs); plot different graphs; and perform the DEGsenrichment with the GO information, pathways visualization andrelated diseases information retrieval. Moreover, KnowSeq is theonly package that allows applying both a machine learning and DEGsenrichment processes just after the DEGs extraction. This ideaemerged with the aim of proposing a complete tool to the researchcommunity containing all the necessary steps to carry out completestudies in a simple and fast way.

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importRdata() and importGTF() now also supports import of RefSeq GFFfiles (downloaded from , see FAQin vignette). This should increase ease of usage for a long range ofspecies not in the Ensembl catalogue.

Fixing R CMD check size error by reducing package size: Brownianbridge distribution, used in the asymptotic implementation ofwasserstein.test now is downloaded into a local cache during thefirst run of wasserstein.test. From there it is loaded in allsubsequent runs. 041b061a72


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  • Melissa Willis
  • Constance Merritt
    Constance Merritt
  • Patrick Martin
    Patrick Martin
  • Hermann Romanov
    Hermann Romanov
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