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The full list of datasets, mapping, and QC statistics is provided in Table S1. Figure 1A shows the distribution of sequencing depth and library complexity for ChIP-seq and control datasets.
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Reference maps were seven soil and landscape datasets mapped at scales ranging from 1 200,000 to 1 5,000,000.
DTXSID datasets mapped to identifiers such as PubChem CIDs can make registration into other databases using CIDs much easier.
A pathway was deemed present when any gene from the above datasets mapped to that pathway.
Since both Pfam and PANTHER provide their datasets mapped to UniProtKB, there is no need to perform any additional mapping.
Regarding the spatial datasets, maps based on global LC datasets agreed less with the reference data than maps based on national LC or satellite data.
Moreover, it is seen cumulatively, that most number of small RNA clusters from all independent datasets map back to Malat1 significantly (Additional File 2).
Using the four transcriptomic datasets mapped onto the PPI network, we detected a total of 162 consistently coexpressed PPI modules ranging in size from 2 to 37 genes [see Fig. S1, Supporting information for a complete overview].
In this study we used a dataset mapping 33,000 large/hollow oaks, habitat for a guild of saproxylic beetles specialised on oaks at an extent of 10,000 km2.
We originally encountered the two biases presented above, as well as two additional biases, in the analysis of a dataset mapping transcriptionally engaged polymerase in the context of exon-intron architecture.
We then demonstrate how both these biases are manifested, and can partially be normalized, in analyzing an NGS dataset mapping transcriptionally engaged RNA polymerases in the context of exon-intron architecture.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com