NEWS.md

In jmw86069/farrisdata: Farris et al Mouse Hippocampus RNA-seq data objects

version 0.0.10.900

changes

• Added EnrichmentDFL which is a list of 12 data.frame objects which each contain gene set enrichment stats results.

version 0.0.9.900

changes

• farris_sashimi_files_df was updated to use more accurate scale_factor values, calculated using housekeepers detected from Salmon gene quantification farrisGenesSE and re-calculated using coverage of each gene exon. For junction files, the junction counts annotated to each housekeeper gene were summed and used for normalization. Intermediate data was reviewed using MA-plots created with the "jamma" package on Github: "jmw86069/jamma".

version 0.0.8.900

changes

• Updated bigWig urls to reference new union coverage files, produced using UCSC bigWigMerge, improved over previous data using bwtool.
• Updated splice junction urls to refer to .gz compressed files, to improve import speed.

version 0.0.7.900

changes

• Changed farris_sashimi_files_df to use union bigWig coverage files to reduce data bandwidth. Added scale_factor values for each coverage file and associated splice junction files. Updated the example docs to show exactly how the files_df data.frame was created.

version 0.0.6.900

bug fixes

• Fixed issue with farris_sashimi_files_df that generated some URL entries which do not exist.

version 0.0.5.900

additions

• farris_sashimi_files_df data.frame was added to support splicejam::prepareSashimi() which uses a data.frame to configure the various input locations for coverage and splice junction files.

version 0.0.4.900

bug fixes

• Added "transcript_id" to colnames(rowData(farrisTxSE))

version 0.0.3.900

bug fixes

• Resolved a small issue in handling negative expression values for normalized TPM data, by adding +1 to all non-zero values. This adjustment ensures that all non-zero TPM values are still positive after normalization, while all values which were originally zero are maintained at zero. Note the TPM thresholds are already adjusted in the jampack Rmarkdown analysis workflow, to accomodate this adjustment.

enhancements

• Full docs were generated using pkgdown, describing each data object.

version 0.0.2.900

New data

• GencodeVM12mm10cai is a numeric vector of codon adaptability index (CAI) values for mouse mm10 Gencode vM12.
• GencodeVM12mm10caiCtLow is an integer count of codons where the CAI value is 0.5 or lower.
• GencodeVM12mm10caiCtBad is an integer count of codons where the CAI value is 0.3 or lower.
• GencodeVM12mm10cai is a numeric vector of codon adaptability index (CAI) values for mouse mm10 Gencode vM12.
• GencodeVM12mm10cdsLength is a numeric vector of CDS lengths for mouse mm10 Gencode vM12.

version 0.0.1.900

New data

• AinsleyGenes, NakayamaGenes, CajigasGenes were added as reference data from three published studies detecting hippocampal CA1 dendrite genes, from mouse, mouse, and rat, respectively. These objects are character vectors of gene symbols.

jmw86069/farrisdata documentation built on Oct. 8, 2019, 9:56 p.m.