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TMM normalization was applied to account for compositional difference between libraries using the function calcNormFactors [ 32].
This value was even greater for comparisons between libraries using the common linker sequence (average Spearman's rho of 0.88) [Additional file 2: Figure S1 and Additional file 5: Table S3], indicating that the common linker reduced biases based on barcode difference, consistent with results reported in [ 9].
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To investigate differences in gene expression profiles, we analyzed genes between both libraries using the IDEG6 modeling methods [ 51].
Signature frequency was also compared statistically between the two libraries using the Z-score method according to Kal et al. [ 34], which uses the p-value and a statistical significance value.
AACR2 comprises a detailed set of rules and guidelines for preparing bibliographic records to represent library resources, established to maintain consistency within the catalog and between the catalogs of libraries using the same code.
MicroRNA-expression levels were tested for significant differential expression between the HTs and EMs libraries using the Limma [ 34] package in R. The Benjamini-Hochberg method (BH-FDR) [ 35] was used to control the false discovery rate.
To compare differentially expressed miRNAs between multiple samples through the miRDeep2-method, read count of each identified miRNA was normalized between libraries using upper-quartile normalization [ 78].
Browse the library using the "Search" screen.
d) Non-metric multidimensional scaling (NMDS) plot based on θ YC distances between libraries extracted using the PowerBiofilm (purple), QuickGene (green) and Maxwell (black) methods from Sample A (squares), B (triangles) and C (circles).
For example, Bansal et al. (2011) [ 36] observed up to a 26% difference in sequencing coverage between libraries captured using the same target capture system.
A web tool IDEG6 was used for detection of differentially expressed genes between two libraries using Fisher exact test [ 91].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com