HTSeq—a Python framework to work with high-throughput sequencing data
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...…https://ccb.jhu.edu/software/tophat/ index.shtml Bowtie2 Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/ bowtie2/index.shtml HTSeq Anders et al., 2015 http://www-huber.embl.de/HTSeq DESeq Anders and Huber, 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html DAVID…...
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...REAGENT or RESOURCE SOURCE IDENTIFIER Cdi V5 This paper N/A Pde8 V5 This paper N/A Camk1-mbl-cherry-camk1 This paper N/A circMbl IRES This paper N/A circPde8 IRES This paper N/A circCdi IRES This paper N/A circTai IRES This paper N/A circMbl IRES reverse This paper N/A circPde8 IRES reverse This paper N/A circCdi IRES reverse This paper N/A circTai IRES reverse This paper N/A UAS-circMbl OE This paper N/A Software and Algorithms Find_circ.py Memczak et al. 2013 http://circbase.org/cgi-bin/ downloads.cgi cORF_prediction_pipeline.py (prediction of ORFs from circRNA sequences) This paper https://github.com/kadenerlab/ cORF_pipeline SRCP.py (short read circRNA pipeline for detection of back-splice reads in RFP RNA-seq) This paper To be published, can be provided upon request Toptat2 Kim et al., 2013 https://ccb.jhu.edu/software/tophat/ index.shtml Bowtie2 Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/ bowtie2/index.shtml HTSeq Anders et al., 2015 http://www-huber.embl.de/HTSeq DESeq Anders and Huber, 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html DAVID Huang da et al., 2009 https://david.ncifcrf.gov/home.jsp...
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...HTSeq-a Python framework to work with high-throughput sequencing data....
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1,249 citations
Cites methods from "HTSeq—a Python framework to work wi..."
...HTSeq–a Python framework to work with high-throughput sequencing data....
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...HTSeq-count (Anders et al., 2015) was used to count the transcripts associated with each gene, and a counts matrix containing the number of counts for each gene across different samples and stimulations was obtained....
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...N/A Mouse: SDHB-deficient: ROSA26-CreERT2/ SDHBfloxed/floxed Laboratory of Eyal Gottlieb N/A Mouse: SDHB-proficient: ROSA26-CreERT2/ SDHBwildtype/wildtype Laboratory of Eyal Gottlieb N/A Sequence-Based Reagents HIF-1a TaqMan assay Applied Biosystems Cat# 4331182; Assay ID: Mm00468869_m1 EGLN3 TaqMan assay Applied Biosystems Cat# 4331182; Assay ID: Mm00472200_m1 Rps18 FAM TaqMan assay Applied Biosystems Cat# 4331182; Assay ID: Mm_02601777_g1 Primers for mouse IL-1b See Table S7 N/A Primers for mouse IL-10 See Table S7 N/A Primers for mouse TNF- a See Table S7 N/A Primers for mouse Rps18 See Table S7 N/A Primers for mouse IL-1ra See Table S7 N/A Primers for mouse PHD3 See Table S7 N/A Primers for mouse cMyc See Table S7 N/A Primers for mouse CD71 See Table S7 N/A Software and Algorithms GraphPad Prism GraphPad Software http://www.graphpad.com/scientific- software/prism/ FlowJo FlowJo http://www.flowjo.com/ Bowtie Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml TopHat Trapnell et al., 2009 http://ccb.jhu.edu/software/tophat/index.shtml HTSeq Anders et al., 2015 https://pypi.python.org/pypi/HTSeq...
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...HTSeq-count was used to count the transcripts associated with each gene in the transcriptomics analysis....
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...…FlowJo http://www.flowjo.com/ Bowtie Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml TopHat Trapnell et al., 2009 http://ccb.jhu.edu/software/tophat/index.shtml HTSeq Anders et al., 2015 https://pypi.python.org/pypi/HTSeq...
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1,244 citations
Cites methods from "HTSeq—a Python framework to work wi..."
...The number of reads mapped to each Ensembl gene (release 72) was counted using the HTSeq python package (Anders et al., 2015), with the ‘union’ overlap resolution mode, and –stranded = no and the expressions of transcripts were quantified as Reads Per Kilobase of exon model per...
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1,206 citations
References
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"HTSeq—a Python framework to work wi..." refers background in this paper
...…is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. functionality from PySam…...
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"HTSeq—a Python framework to work wi..." refers methods in this paper
...These counts can then be used for gene-level differential expression analyses using methods such as DESeq2 (Anders and Huber, 2010) or edgeR (Robinson et al., 2010)....
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18,858 citations
"HTSeq—a Python framework to work wi..." refers background in this paper
...Interval queries are a recurring task in HTS analysis problems, and several libraries now offer solutions for different programming languages, including BEDtools (Quinlan and Hall, 2010; Dale et al., 2011) and IRanges/GenomicRanges (Lawrence et al....
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...Interval queries are a recurring task in HTS analysis problems, and several libraries now offer solutions for different programming languages, including BEDtools (Quinlan and Hall, 2010; Dale et al., 2011) and IRanges/GenomicRanges (Lawrence et al., 2013)....
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