HTSeq—a Python framework to work with high-throughput sequencing data
TLDR
This work presents HTSeq, a Python library to facilitate the rapid development of custom scripts for high-throughput sequencing data analysis, and presents htseq-count, a tool developed with HTSequ that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.Abstract:
Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. Availability and implementation: HTSeq is released as an opensource software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq. Contact: sanders@fs.tum.deread more
Citations
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E-cadherin is required for metastasis in multiple models of breast cancer.
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TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection.
Francesca Alfei,Kristiyan Kanev,Maike Hofmann,Ming Wu,Hazem E. Ghoneim,Hazem E. Ghoneim,Patrick Roelli,Patrick Roelli,Patrick Roelli,Daniel T. Utzschneider,Madlaina von Hoesslin,Jolie G. Cullen,Yiping Fan,Vasyl Eisenberg,Dirk Wohlleber,Katja Steiger,Doron Merkler,Mauro Delorenzi,Mauro Delorenzi,Percy A. Knolle,Cyrille J. Cohen,Robert Thimme,Benjamin Youngblood,Dietmar Zehn +23 more
TL;DR: It is shown that TOX is a critical factor for the normal progression of T cell dysfunction and the maintenance of exhausted T cells during chronic infection, and provide a link between the suppression of effector function intrinsic to CD8 T cells and protection against immunopathology.
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Neural Circuit-Specialized Astrocytes: Transcriptomic, Proteomic, Morphological, and Functional Evidence
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TL;DR: In this article, the authors used multiple integrated approaches, including RNA sequencing (RNA-seq), mass spectrometry, electrophysiology, immunohistochemistry, serial block-face-scanning electron microscopy, morphological reconstructions, pharmacogenetics, and diffusible dye, calcium, and glutamate imaging, to directly compare adult striatal and hippocampal astrocytes under identical conditions.
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The tumor microenvironment underlies acquired resistance to CSF-1R inhibition in gliomas
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An atlas of genetic influences on osteoporosis in humans and mice
John A. Morris,John P. Kemp,John P. Kemp,Scott E. Youlten,Laetitia Laurent,John G. Logan,Ryan C. Chai,Nicholas A. Vulpescu,Vincenzo Forgetta,Aaron Kleinman,Sindhu T. Mohanty,C. Marcelo Sergio,Julian M.W. Quinn,Loan Nguyen-Yamamoto,Aimee Lee Luco,Jinchu Vijay,Marie-Michelle Simon,Albena Pramatarova,Carolina Medina-Gomez,Katerina Trajanoska,Elena J. Ghirardello,Natalie C. Butterfield,Katharine F. Curry,Victoria D. Leitch,Penny C. Sparkes,Anne-Tounsia Adoum,Naila S. Mannan,Davide Komla-Ebri,Andrea S. Pollard,Hannah F. Dewhurst,Thomas A D Hassall,Michael-John G. Beltejar,Douglas J. Adams,Suzanne M. Vaillancourt,Stephen Kaptoge,Paul A. Baldock,Cyrus Cooper,Cyrus Cooper,Cyrus Cooper,Jonathan Reeve,Evangelia E. Ntzani,Evangelia E. Ntzani,Evangelos Evangelou,Evangelos Evangelou,Claes Ohlsson,David Karasik,Fernando Rivadeneira,Douglas P. Kiel,Jonathan H Tobias,Celia L Gregson,Nicholas C. Harvey,Nicholas C. Harvey,Elin Grundberg,Elin Grundberg,David Goltzman,David J. Adams,Christopher J. Lelliott,David A. Hinds,Cheryl L. Ackert-Bicknell,Yi-Hsiang Hsu,Matthew T. Maurano,Peter I. Croucher,Graham R. Williams,J. H. Duncan Bassett,David M. Evans,David M. Evans,J. Brent Richards +66 more
TL;DR: This genetic atlas provides evidence linking associated SNPs to causal genes, offers new insight into osteoporosis pathophysiology, and highlights opportunities for drug development.
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