HTSeq—a Python framework to work with high-throughput sequencing data
Citations
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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References
379 citations
"HTSeq—a Python framework to work wi..." refers background in this paper
...…represent genomic coordinates or intervals, and these are guaranteed to always follow a fixed convention (namely, following Python conventions, zero-based, with intervals being half-open), and parser classes take care to apply appropriate conversion when the input format uses different convention....
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83 citations
55 citations
"HTSeq—a Python framework to work wi..." refers background or methods in this paper
...This has been implemented in C++, building on the map template of the C++ standard library, which is typically realized as a red–black tree (Josuttis, 1999)....
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...…represent genomic coordinates or intervals, and these are guaranteed to always follow a fixed convention (namely, following Python conventions, zero-based, with intervals being half-open), and parser classes take care to apply appropriate conversion when the input format uses different convention....
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21 citations
"HTSeq—a Python framework to work wi..." refers methods in this paper
...In a recent benchmark, Fonseca et al. (2014) compared htseq-count with these other counting tools and judged the accuracy of htseq-count favourably....
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