NEWS.md

In SU-CompBio/SplicingFactory: Splicing Diversity Analysis for Transcriptome Data

SplicingFactory 1.3.1 (dev)

• Citation update
• Other minor corrections

SplicingFactory 1.0.3 (stable)

• Bug fix for example data.
• Other minor changes.

SplicingFactory 1.0.2 (stable)

• Bug fix for single sample analysis.

SplicingFactory 1.0.1 (stable)

• Updates to URL, email and citation.

SplicingFactory 0.99.21 (dev)

• Updated lists of gene names and TCGA sample IDs in tcga_brca_luma_dataset.RData.

SplicingFactory 0.99.20 (dev)

• Created new dataset with another random seed in tcga_brca_luma_dataset.RData.

SplicingFactory 0.99.19 (dev)

• Added lists of gene names and TCGA sample IDs in tcga_brca_luma_dataset.RData.

SplicingFactory 0.99.18 (dev)

• R version update.

SplicingFactory 0.99.17 (dev)

• Minor corrections.

SplicingFactory 0.99.16 (dev)

• Minor corrections.

SplicingFactory 0.99.15 (dev)

• Adjust sample dataset creating script to the use of SummarizedExperiment.

SplicingFactory 0.99.14 (dev)

• Documentation updates.

SplicingFactory 0.99.13 (dev)

• SummarizedExperiment input for calculate_difference.
• Changed SE_assay parameter name to assayno.
• Documentation and example updates.

SplicingFactory 0.99.12 (dev)

• Documentation and example updates.

SplicingFactory 0.99.11 (dev)

• SummarizedExperiment corrections.
• Vignette updates.

SplicingFactory 0.99.10 (dev)

• SummarizedExperiment output for calculate_diversity.
• Vignette updates.
• Example dataset updates.

SplicingFactory 0.99.9 (dev)

• Documentation and code formatting updates.

SplicingFactory 0.99.8 (dev)

• Examples for diversity calculation functions.

SplicingFactory 0.99.7 (dev)

• More flexible single calculate_entropy function instead of separate naive and Laplace entropy.
• P-value correction method can be set by user.
• Formatting corrections.

SplicingFactory 0.99.5 (dev)

• Updated DESCRIPTION.
• Formatting corrections.
• Corrected bug in data description.
• Updated methods for obtaining class of input.
• Added verbose argument for functions.

SplicingFactory 0.99.4 (dev)

• Code and documentation formatting corrections.
• Updates to example dataset.

SplicingFactory 0.99.3 (dev)

• SummarizedExperiment input type updated in calculate_diversity, new argument: SE_assay.

• Documentation, vignette updated.

SplicingFactory 0.99.2 (dev)

• SummarizedExperiment input type instead of ExpressionSet.

SplicingFactory 0.99.1 (dev)

• Correction: unnecessary file removed.

SplicingFactory 0.99.0 (dev)

• Submitted to Bioconductor.

SU-CompBio/SplicingFactory documentation built on March 28, 2022, 4:39 a.m.