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Recent Releases of nanostringr

nanostringr - nanostringr 0.6.1

  • allow normalization of pools from same CodeSet as the reference pools, e.g. when we want to normalize cross-site replicates. Add parameter same_codeset to normalize_pools() so we can use a different file name pattern to match for these pools.

- R
Published by dchiu911 9 months ago

nanostringr - nanostringr 0.6.0

  • Replace magrittr pipe with native pipe, subsequently increase minimum R version to 4.2
  • Update read_rcc() to replace gene names PD1 with PD-1 and PDL1 with PD-L1

- R
Published by dchiu911 10 months ago

nanostringr - nanostringr 0.5.0

  • Fix normalize_pools() and normalize_random() functions so they actually work
  • Remove magrittr from Suggests
  • Remove deprecated usage of .data

- R
Published by dchiu911 about 1 year ago

nanostringr - 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.

- R
Published by dchiu911 over 1 year ago

nanostringr - 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

- R
Published by dchiu911 over 2 years ago

nanostringr - 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()

- R
Published by dchiu911 over 3 years ago

nanostringr - 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

- R
Published by dchiu911 almost 4 years ago

nanostringr - 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()

- R
Published by dchiu911 about 5 years ago

nanostringr - 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

- R
Published by dchiu911 almost 7 years ago

nanostringr - 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

- R
Published by dchiu911 almost 7 years ago

nanostringr - 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

- R
Published by dchiu911 almost 7 years ago

nanostringr - nanostringr 0.1.1

  • update citation to link to PLOS paper

- R
Published by dchiu911 almost 7 years ago

nanostringr - nanostringr 0.1.0

  • Added a NEWS.md file to track changes to the package.

- R
Published by dchiu911 almost 7 years ago