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The fourth module generates counts of positive storyline scores for each classifier that are above the threshold.
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This generates count-based miRNA expression data for subsequent statistical analysis.
In this way, the SIMIND program continuously maintains an accurate relation between the number of histories generating counts in the projection images and the underlying activity in a particular voxel in the source volume.
The sampling areas were separated by x y steps of 296.7 µm×296.7 µm, generating counts of 150 300 sampled cells per animal.
On the basis of the hierarchical model, we generate counts for a particular Tuesday, say, as follows.
From the combined dataset, we generated counts of casualties and collisions for each road segment and year.
All ChIP-seq and RNA-seq data were processed with RepEnrich to generate counts for all repetitive element subfamilies.
Matching locations were subsequently used to generate counts for identified ERVs and Ensemble-provided coding sequences (Bos_taurus.Btau_4.0.55.gtf.gz).
These mappings of full length reads and junction-reads were subsequently used by Cufflinks [ 42] to generate counts and coverages for annotated genes and their transcripts, all of whose annotations were retrieved from the 5.29 release of Flybase.
To test how RNA transcripts tend to be expressed across region types, we generated counts of the number of times an RNA is detectable across the 10 regions and stratified this by transcript-type based on GENCODE-lncipedia annotations.
To identify differential expression patterns, the sequenced reads from each sample were then analyzed independently using Cufflinks to generate counts and coverage for seed-expressed genes and their isoforms.
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