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catalyst

Cytometry dATa anALYsis Tools

clme

Constrained Linear Mixed Effects

colorjam

coverjam

Genome sequence coverage heatmaps around a central genome feature, such as transcript start site (TSS) or ChIP-seq/ATAC-seq peaks; or across a scaled genome region, such as gene locus regions from transcript start site (TSS) to transcript termination site (TTS).

farrisdata

genejam

Gene annotation utility functions, gene aliases, updating gene symbols to the most current official symbol.

jamba

Jam Base Methods for R

jamma

Jam MA-plots, volcano plots, other relevant genomics visualizations

jampack

Jam R package suite for omics data analysis

jamses

Jam SummarizedExperiment Stats (jamses), methods for experiment design, statistical contrast, differential analysis, and visualization of experiment design.

jamsession

Manage R sessions, objects, project-specific functions

mirnapath

miRNApath: Pathway Enrichment for miRNA Expression Data

multienrichjam

Analysis and Visualization of Multiple Gene Set Enrichments

myd88-asthma

neurojam

pajam

Protein Atlas tissue and cell atlas data and visualization in R from https://proteinatlas.org

peakdistanceenrichment

ATACseq peak enrichment with sliding scale distance to genes

platjam

Platform data import and manipulation for Jam packages.

rmarkdown

Dynamic Documents for R

salsa

Single-cell Amalgamation by Latent Semantic Analysis (SALSA)

somadataio

The SomaDataIO package loads the SomaLogic, Inc. proprietary data file, called an ADAT file ('*.adat'). It also provides auxiliary functions for extracting and manipulating relevant information from an ADAT, as well as exporting a modified ADAT to file.

splicejam

Sashimi plots for RNA-seq data using detected transcripts

svn-color

a wrapper script to colorize SVN output

venndir

Venn diagrams with directionality (concordance), optional display of items inside the figure, text Venn diagrams