HTSeq—a Python framework to work with high-throughput sequencing data
Citations
2,276 citations
1,963 citations
Cites methods from "HTSeq—a Python framework to work wi..."
...The simplest approach to quantification is to aggregate raw counts of mapped reads using programs such as HTSeq-count [35] or featureCounts [36]....
[...]
...This application is primarily based on the number of reads that map to each transcript sequence, although there are algorithms such as Sailfish that rely on k-mer counting in reads without the need for mapping [34]....
[...]
...These methods allocate multi-mapping reads among transcript and output within-sample normalized values corrected for sequencing biases [35, 41, 43]....
[...]
...Algorithms that quantify expression from transcriptome mappings include RSEM (RNA-Seq by Expectation Maximization) [40], eXpress [41], Sailfish [35] and kallisto [42] among others....
[...]
1,865 citations
1,741 citations
1,642 citations
References
47,038 citations
45,957 citations
"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…...
[...]
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)....
[...]
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....
[...]
...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)....
[...]