NEWS.md

In NADfinder: Call wide peaks for sequencing data

CHANGES IN VERSION 1.11.1

• replace all class by is.

CHANGES IN VERSION 1.9.2

• Update citation.
• Update trimPeaks.R to filter peaks using adjusted pvalues and trimmed peaks by removing windows with zscore < 1.696

CHANGES IN VERSION 1.9.1

• Add citation.

CHANGES IN VERSION 1.7.4

• Fix the warning of documentation of computeLibSizeChrom.

CHANGES IN VERSION 1.7.1

• Update author email.

CHANGES IN VERSION 1.5.4

• Fix the warning of documentation in windows with missing link.

CHANGES IN VERSION 1.5.3

• add BiocManager into suggest package.

CHANGES IN VERSION 1.3.13

• add tileCount2.

CHANGES IN VERSION 1.3.12

• update callPeaks.

CHANGES IN VERSION 1.3.11

• update documentation of NADfinder.

CHANGES IN VERSION 1.3.10

• Update the callPeaks.
• Fix typo of nucleolus.

CHANGES IN VERSION 1.3.9

• Fix the warning in windows for the help files.

CHANGES IN VERSION 1.3.8

• update the documentation of tileCount, log2se and trimPeaks

CHANGES IN VERSION 1.3.5

• Speed up tileCount per Herve's recommendation
• Add Herve Pages as a coauthor
• resave triplicate.count and single.count

CHANGES IN VERSION 1.3.3

• Fix the warning in windows for the help files.
• Add Haibo Liu as a coauthor.
• Add different methods for transformation and combining p-values.

CHANGES IN VERSION 1.3.1

• remove Bessel's correction for zscore calculation
• narrow the distance when trim the peaks to avoid overlaps.
• change the baseline.modpolyfit from degree 4 to degree 3.

CHANGES IN VERSION 1.1.2

• update the documentations.

CHANGES IN VERSION 1.1.1

• add parameter in backgroundCorrection.

CHANGES IN VERSION 0.99.4

• replace slidingWindows by GenomicRanges::slidingWindows

CHANGES IN VERSION 0.99.3

• add new function cumulativePercentage
• add DNASeq, PeakDetection to biocViews.
• update documentations of vignette by provide a narrative better explaining use of the package.
• indicate argument type for each parameter in the documentations.
• use vectorized rather than iteractive operations in place of other uses of apply()
• use seq_len and seq_along to replace :

CHANGES IN VERSION 0.99.2

• change GRanges to RangedSummarizedExperiment
• update documentations
• change plotCorrelations to getCorrelations
• change sig2bedgraph to exportSignals
• change tileGRanges to slidingWindows

CHANGES IN VERSION 0.99.1

• change NEWS to NEWS.md
• add details to README.md
• update documentations

CHANGES IN VERSION 0.99.0

• update the version to 0.99.0

CHANGES IN VERSION 0.1.4

• add new function plotSig

CHANGES IN VERSION 0.1.3

• add new function plotCorrelations

CHANGES IN VERSION 0.1.2

• add new authors.

CHANGES IN VERSION 0.1.1

• add the power to analyze duplicates.

CHANGES IN VERSION 0.1.0

• Create the package.

NADfinder documentation built on Nov. 8, 2020, 5:35 p.m.