Package: blacksheepr 1.21.0

RugglesLab

blacksheepr: Outlier Analysis for pairwise differential comparison

Blacksheep is a tool designed for outlier analysis in the context of pairwise comparisons in an effort to find distinguishing characteristics from two groups. This tool was designed to be applied for biological applications such as phosphoproteomics or transcriptomics, but it can be used for any data that can be represented by a 2D table, and has two sub populations within the table to compare.

Authors:MacIntosh Cornwell [aut], RugglesLab [cre]

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blacksheepr.pdf |blacksheepr.html✨
blacksheepr/json (API)
NEWS

# Install 'blacksheepr' in R:

install.packages('blacksheepr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ruggleslab/blacksheepr/issues

Datasets:

sample_annotationdata - Sample_annotationdata
sample_phosphodata - Sample_phosphodata
sample_rnadata - Sample_rnadata

On BioConductor:blacksheepr-1.19.0(bioc 3.21)blacksheepr-1.20.0(bioc 3.20)

sequencing rnaseq geneexpression transcription differentialexpression transcriptomics

4.30 score 6 scripts 198 downloads 11 exports 123 dependencies

Last updated 25 days agofrom:4a716903d7. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	NOTE	Nov 19 2024
R-4.5-linux	NOTE	Nov 19 2024
R-4.4-win	NOTE	Nov 19 2024
R-4.4-mac	NOTE	Nov 19 2024
R-4.3-win	OK	Nov 19 2024
R-4.3-mac	OK	Nov 19 2024

Exports:annotationlist_builder comparison_groupings count_outliers create_heatmap deva deva_normalization deva_results make_comparison_columns make_outlier_table outlier_analysis outlier_heatmap

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl DBI dbplyr DelayedArray DESeq2 DEXSeq digest doParallel dplyr fansi farver fastmap filelock foreach formatR futile.logger futile.options genefilter geneplotter generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggplot2 GlobalOptions glue gridExtra gtable hms httr httr2 hwriter IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pasilla pillar pkgconfig plogr png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo Rhtslib rjson rlang Rsamtools RSQLite S4Arrays S4Vectors scales shape snow SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridis viridisLite withr XML xml2 xtable XVector zlibbioc

Outlier Analysis using blacksheepr

MacIntosh Cornwell

Rendered fromblacksheepr_vignette.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2019-10-11
Started: 2019-10-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create the annotation object for plotting in a heatmap	annotationlist_builder
Create all of the groups based on the input metadata	comparison_groupings
Count up the outlier information for each of the groups you have made. If aggregating then you will have to turn the parameter on, but you still input the outliertable. Aggregate will count the total number of outliers AND nonoutliers in its operation, so it needs the original outlier table made by the <make_outlier_table> function.	count_outliers
Plot out a heatmap	create_heatmap
Run the entire blacksheep Function from Start to finish	deva
Normalization of data to prepare for deva. Uses a Median of Ratio method followed by a log2 transformation.	deva_normalization
Utility function that allows easier grabbing of data	deva_results
Utility function that will take in columns with several subcategories, and output several columns each with binary classifications. ex) col1: A,B,C >> colA: A,notA,notA; colB: notB,B,notB; colC: notC,notC,C	make_comparison_columns
Separate out the "i"th gene, take the bounds, and then create a column that says whether or not this gene is high, low, or none in a sample with regards to the other samples in the dataset. Repeat this for every gene to create a reference table.	make_outlier_table
With the grouptablist generated by count_outliers - run through and run a fisher exact test to get the p.value for the difference in outlier count for each feature in each of your comparisons	outlier_analysis
With the grouptablist generated by count_outliers - run through and run a fisher exact test to get the p.value for the difference in outlier count for each feature in each of your comparisons	outlier_heatmap
sample_annotationdata	sample_annotationdata
sample_phosphodata	sample_phosphodata
sample_rnadata	sample_rnadata