NEWS.md

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

CHANGES IN VERSION 1.19.1

• Update email address.

CHANGES IN VERSION 1.17.1

• allow DNAStringSet for genome.

CHANGES IN VERSION 1.13.15

• add normalizeTEbyLoess functions.

CHANGES IN VERSION 1.13.14

• simplify the normBy and translationalEfficiency functions.

CHANGES IN VERSION 1.13.13

• update translationalEfficiency with shrink method.

CHANGES IN VERSION 1.13.12

• update condonBias function.

CHANGES IN VERSION 1.13.11

• fix the seqlevels style issue for coverageDepth.

CHANGES IN VERSION 1.13.10

• update the codonUsage

CHANGES IN VERSION 1.13.9

• fix the strand issue for readsEndPlot.
• change the output for multiple functions.

CHANGES IN VERSION 1.13.8

• update vignettes.

CHANGES IN VERSION 1.13.7

• add parameter removeDuplicates for codonBias.

CHANGES IN VERSION 1.13.6

• fix a issue in codonUsage.
• update the summary output for codonBias.

CHANGES IN VERSION 1.13.5

• add function codonBias.

CHANGES IN VERSION 1.13.4

• fix the bug for getFPKM.

CHANGES IN VERSION 1.13.3

• import txdbmaker

CHANGES IN VERSION 1.13.2

• fix the bug the estimatePsite did not pass ignore.seqlevelsStyle to assignReadingFrame function.

CHANGES IN VERSION 1.13.1

• add ignore.seqlevelsStyle parameter to provide the flexibility of seqlevels.

CHANGES IN VERSION 1.11.1

• add precedence parameter to readsDistribution

CHANGES IN VERSION 1.7.1

• export readLen for estimatePsite.

CHANGES IN VERSION 1.3.4

• add rmarkdown as suggest package.

CHANGES IN VERSION 1.3.3

• add github action.

CHANGES IN VERSION 1.3.2

• fix the issue if there is softclip in the mapping reads and the reads length is smaller than shfit range.

CHANGES IN VERSION 1.3.1

• keep the raw counts for countReads.

CHANGES IN VERSION 1.1.6

• fix the issue in shiftReads for reads width and readsEndPlot for seqlevels.

CHANGES IN VERSION 1.1.5

• Update documentation about the R version requirement.

CHANGES IN VERSION 1.1.4

• Update authorship.

CHANGES IN VERSION 1.1.3

• Fix the error "CIGAR is empty after qnarrowing".

CHANGES IN VERSION 1.1.2

• update vignette to fix the typos.
• update plotTranscript to give more informative warning message.

CHANGES IN VERSION 1.1.1

• update vignette by adding background colors for better understanding the pipeline.

CHANGES IN VERSION 0.99.91

• change Y-axis lable from Frequence to Frequency for plot Distance2Codon.
• update vignette.

CHANGES IN VERSION 0.99.9

• reset the test_estimatePsite.

CHANGES IN VERSION 0.99.8

• decrease the testing time.

CHANGES IN VERSION 0.99.6

• fix the warning missing link of plot in plotTE.

CHANGES IN VERSION 0.99.5

• update ggBar function to accept more colors.
• update readsEndPlot function with shift parameter.
• update plotDistance2Codon function with a range of plot window
• add codonUsage function.

CHANGES IN VERSION 0.99.4

• update the description in DESCRIPTION.
• update help files.

CHANGES IN VERSION 0.99.3

• change the link from AtomicList to AtomicList-class and RUVs-methods to RUVs.
• shorter lines < 80 characters.
• spead up coverageDepth

CHANGES IN VERSION 0.99.2

• remove .DS_Store

CHANGES IN VERSION 0.99.1

• decrease the size of the package
• simplify and add parameter anchor for the estimatePsite function.
• add parameter normByLibSize for function translationalEfficiency
• add more test files.
• update documentations.

CHANGES IN VERSION 0.99.0

• Submit to Bioconductor.

CHANGES IN VERSION 0.0.6

• Remove sapply.

CHANGES IN VERSION 0.0.1

• Create the package.

jianhong/ribosomeProfilingQC documentation built on Jan. 6, 2025, 10:01 a.m.