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atenrich

Interface for scoring enrichment of gene lists from a database of functional genomic experiments in Arabidopsis.

circa_pyplot

Plots timeseries data (e.g. gene expression) with circadian or diurnal light/dark bars on the x-axis, using the matplotlib library in Python.

corrall

corrall (CORRelation analysis of ALLele-specific expression) provides tools for aggregating GATK allele-specific expression output across sets of SNPs and individuals.

frameworkmodel

genelistdb

Basic scripting to create mySQL database storing Arabidopsis gene lists from publications (e.g. lists of differentially expressed genes in mutants or treatments, lists of promoters identified as bound by ChIP-seq).

limix_tools

Tools for working with the LIMIX linear mixed modelling package.

merge_featurecounts

Merge featurecounts outputs across thousands of files.

mmb_exemplar_model

MATLAB code to simulate models used in Seaton, Methods in Molecular Biology, 2016, "ODE-based modeling of complex regulatory circuits".

pufferfish

Yummie deep fried pufferfish

seaton2018_phya_photoperiod_model

Matlab code to simulate the model of phyA dynamics for "Dawn and photoperiod sensing by phytochrome A", Seaton et al, 2018.

tequant

Tools for manipulating quantification of transposable element reads from RNA-seq data.