NEWS.md

In nanostringr: Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data

nanostringr 0.4.2

• Fix bug in NanoStringQC() where the signal to noise ratio input threshold was not being compared against the observed SNR because the parameter name was the same as the column name. Hence the comparison was against itself, and normFlag only checked the percent of genes detected.

nanostringr 0.4.1

• Fix warning regarding old-style CITATION
• Add ORCID to package authors
• Use GitHub Actions for pkgdown site
• use stricter R CMD check standard workflow
• decrease package dependencies: removed epiR, forcats, tibble from Imports, moved magrittr to Suggests

nanostringr 0.4.0

• new normalize_pools() function to use common pool samples to correct for batch effects when normalizing
• new normalize_random() function to use randomly selected samples as the reference for refMethod()

nanostringr 0.3.0

• fix calculation of genes detected so that the limit of detection is compared in parallel to each sample's counts instead of being recycled, #20

• use GitHub Actions for CI, replacing Travis and Appveyor

• add gene label "PC_1" for checking smallest positive control

• more robust extraction of numeric concentrations from PC gene labels

nanostringr 0.2.0

• use RCC file names in parsed data of read_rcc(). Also rename gene name CD3E to CD3e for compatibility purposes

• update roxygen

• remove Rplots.pdf generated from tests, removed deprecated context()

nanostringr 0.1.4

• reduce package dependencies from Imports

• remove old packages from Suggests

• performance gains in refMethod()

• raw parameter in NanoStringQC() now accepts tibbles

nanostringr 0.1.3

• check for presence of "Positive" and "Negative" genes in NanoStringQC()

• remove most code lints

• unit tests for read_rcc() and internal functions check_colnames(), check_genes()

• fix bug using NanoStringQC() for single sample data

nanostringr 0.1.2

• sort sample names in HLD and OVD cohorts by numeric order, not lexicographic order

• tidy up code in HKnorm()

• use tidy evaluation in NanostringQC()

• use vapply() over sapply() for input checking functions

nanostringr 0.1.1

• update citation to link to PLOS paper

nanostringr 0.1.0

• New submission to CRAN accepted on March 15, 2019

nanostringr documentation built on June 22, 2024, 10:17 a.m.