NEWS.md

In tpq/miSciTools: Miscellaneous Science Tools for Bioinformatic Analysis

miSciTools 1.1.9

• New helper functions
  • New ensg2hgnc and hgnc2ensg functions convert genes to genes
  • New ensg2go and hgnc2go functions convert genes to GO IDs
  • New go2term function converts GO IDs to GO terms
  • New hgnc2liger function runs liger GSEA

miSciTools 1.1.8

• New helper functions
  • New replaceNA function replaces all NAs in vector or data.frame
  • New remove_geom removes a GEOM layer from a ggplot object
  • New quick.anova runs an ANOVA using f(x, y) syntax
• Update fig methods
  • New dir argument allows user to set output directory

miSciTools 1.1.7

• New helper functions
  • New test.lequal tests whether all elements in a list are equal
  • New randSamps randomly assigns class labels
  • New randBoots indexes bootstraps of samples
  • New randFolds indexes folds of samples
• Update quick.edgeR
  • New norm.method argument selects normalization method
• Update quick.DESeq2
  • Add drop = FALSE to avoid error

miSciTools 1.1.6

• Update quick.edgeR
  • No longer removes tags with FDR > 0.05
• Update demand
  • Now uses BiocManager::install()

miSciTools 1.1.5

• Add fig methods

miSciTools 1.1.4

• Update data
  • Add ctd.wide data which explodes "InteractionActions" column
  • Update ctd data

miSciTools 1.1.3

• Add fs methods
  • Migrate fsPathClassRFE and fsSelbal from exprso

miSciTools 1.1.2

• Add fs methods
  • New fsPropd module selects features using propr::propd
  • New fsPRA module selects features using propr::pra
• Add methods
  • New rda.reconstruct reconstructs data from RDA object
  • New wwtest resembles tttest but non-parametric

miSciTools 1.1.1

• Revise getRecount function
  • Make getRecount more reliable

miSciTools 1.1.0

• Add methods
  • New getRecount retrieves data from recount2 server

miSciTools 1.0.9

• Add methods
  • New quick.DESeq2 function performs formula-based DE analysis
  • New wide2long and long2wide functions convert between data styles
  • New tttest function to make t-test tables from long data

miSciTools 1.0.8

• Revise aptly function
  • Delineate mean and total lengths for found structures
  • Allow user to append additional RNAfold arguments
  • Characterize left and right bulges

miSciTools 1.0.7

• Implemented aptly function
  • Procedurally characterizes RNA sequences based on secondary structure
  • Fixed bug caused by absence of any secondary structure

miSciTools 1.0.6

• Implemented fastafolder function
  • Calculates the dissimilarity between sequences based on secondary structure
• Added packageCheck function
  • Triggers an error if a package is not installed

miSciTools 1.0.5

• Update ctd data and remove NA GeneIDs

miSciTools 1.0.4

• Implemented quick.edgeR function
  • Run edgeR Exact Test for differential expression analysis
• Added kegg data
  • Details KEGGREST-gene relationships

miSciTools 1.0.3

• Have simpliGSEA pass alternative argument to fisher.test

miSciTools 1.0.2

• Have migraph functions coerce arguments as character input
• Fix errors in documentation and package imports
• Fix simpliGSEA pruning so it actually works
• Add code for progress bar function

miSciTools 1.0.1

• Modified simpliGSEA function
  • Now prunes genes missing in universe or database
• Implemented migraph functions
  • New migraph.add adds vertices or edges to graph
  • New migraph.color colors vertices or edges
  • New migraph.clean cleans graph to plot

miSciTools 1.0.0

• Implemented lift function
  • "Lifts over"" coordinates from one genome build to another
• Implemented simpliGSEA function
  • Performs gene set enrichment analysis for non-DAG
• Implemented multiplot function
  • Quickly plots multiple figures in the same figure
  • Source: http://www.cookbook-r.com/
• Implemented demand function
  • Looks for and installs package from multiple sources
• Implemented asTempObj function
  • Sets value as a random but unique variable name
• Implemented writeR function
  • Writes an R script as a temporary file
• Implemented qsub function
  • Sends a system command through qsub
• Implemented insert function
  • Inserts a new line of text into an existing file
• Added ctd data
  • Details chemical-gene interactions
• Added linc2go data
  • A GeneSetCollection for lincRNA

tpq/miSciTools documentation built on Sept. 16, 2019, 4:43 p.m.