HTSeq—a Python framework to work with high-throughput sequencing data
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47,038 citations
Cites background from "HTSeq—a Python framework to work wi..."
...de/ users/anders/HTSeq, described in [9] a user would typically just provide a path, e....
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...## [1] "gene" "baseMean" "baseVar" "allZero" ## [5] "dispGeneEs" "dispFit" "dispersion" "dispIter" ## [9] "dispOutlie" "dispMAP" "Intercept" "conditionu" ## [13] "conditiont" "SE_Interce" "SE_conditi" "SE_conditi" ## [17] "MLE_Interc" "MLE_condit" "WaldStatis" "WaldStatis" ## [21] "WaldStatis" "WaldPvalue" "WaldPvalue" "WaldPvalue" ## [25] "betaConv" "betaIter" "deviance" "maxCooks"...
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22,147 citations
Cites methods from "HTSeq—a Python framework to work wi..."
...Raw read counts are assembled outside limma using tools such as featureCounts (29), HTSeq-counts (30) or RSEM (31)....
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17,014 citations
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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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39,291 citations
29,413 citations
"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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