pmparser - Create and Maintain a Relational Database of Data from PubMed/MEDLINE

Provides a simple interface for extracting various elements from the publicly available PubMed XML files, incorporating PubMed's regular updates, and combining the data with the NIH Open Citation Collection. See Schoenbachler and Hughey (2021) <doi:10.7717/peerj.11071>.

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5.98 score 19 stars 1 scripts 179 downloads

limorhyde2 - Quantify Rhythmicity and Differential Rhythmicity in Genomic Data

Fit linear models based on periodic splines, moderate model coefficients using multivariate adaptive shrinkage, then compute properties of the moderated curves.

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4.78 score 1 stars 2 scripts 224 downloads

simphony - Simulating Large-Scale, Rhythmic Data

A tool for simulating rhythmic data: transcriptome data using Gaussian or negative binomial distributions, and behavioral activity data using Bernoulli or Poisson distributions. See Singer et al. (2019) <doi:10.7717/peerj.6985>.

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rhythmic-datasimphony

4.78 score 3 stars 2 scripts 232 downloads

limorhyde - Differential Analysis of Rhythmic Transcriptome Data

A flexible approach, inspired by cosinor regression, for differential analysis of rhythmic transcriptome data. See Singer and Hughey (2018) <doi:10.1177/0748730418813785>.

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4.00 score 2 stars 6 scripts 245 downloads

seeker - Simplified Fetching and Processing of Microarray and RNA-Seq Data

Wrapper around various existing tools and command-line interfaces, providing a standard interface, simple parallelization, and detailed logging. For microarray data, maps probe sets to standard gene IDs, building on 'GEOquery' Davis and Meltzer (2007) <doi:10.1093/bioinformatics/btm254>, 'ArrayExpress' Kauffmann et al. (2009) <doi:10.1093/bioinformatics/btp354>, Robust multi-array average 'RMA' Irizarry et al. (2003) <doi:10.1093/biostatistics/4.2.249>, and 'BrainArray' Dai et al. (2005) <doi:10.1093/nar/gni179>. For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and quality trimming using 'TrimGalore' Krueger <https://github.com/FelixKrueger/TrimGalore>, performs quality control checks using 'FastQC' Andrews <https://github.com/s-andrews/FastQC>, quantifies transcript abundances using 'salmon' Patro et al. (2017) <doi:10.1038/nmeth.4197> and potentially 'refgenie' Stolarczyk et al. (2020) <doi:10.1093/gigascience/giz149>, aggregates the results using 'MultiQC' Ewels et al. (2016) <doi:10.1093/bioinformatics/btw354>, maps transcripts to genes using 'biomaRt' Durinkck et al. (2009) <doi:10.1038/nprot.2009.97>, and summarizes transcript-level quantifications for gene-level analyses using 'tximport' Soneson et al. (2015) <doi:10.12688/f1000research.7563.2>.

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3.78 score 3 stars 1 scripts 121 downloads

zeitzeiger - Regularized Supervised Learning for Data from Rhythmic Systems

Method for predicting the value of a periodic variable from a high-dimensional observation. See Hughey et al. (2016) <doi:10.1093/nar/gkw030> and Hughey (2017) <doi:10.1186/s13073-017-0406-4>.

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3.78 score 12 stars 2 scripts

phers - Calculate Phenotype Risk Scores

Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and rare genetic variants. See Bastarache et al. 2018 <doi:10.1126/science.aal4043>.

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3.30 score 1 scripts 134 downloads

deltaccd - Quantify Rhythmic Gene Co-Expression Relative to a Reference

Infer progression of circadian rhythms in transcriptome data in which samples are not labeled with time of day and coverage of the circadian cycle may be incomplete. See Shilts et al. (2018) <doi:10.7717/peerj.4327>.

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3.00 score 1 stars 4 scripts 200 downloads

tipa - Tau-Independent Phase Analysis for Circadian Time-Course Data

Accurately estimates phase shifts by accounting for period changes and for the point in the circadian cycle at which the stimulus occurs. See Tackenberg et al. (2018) <doi:10.1177/0748730418768116>.

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2.70 score 217 downloads

spectr - Calculate the Periodogram of a Time-Course

Provides a consistent interface to use various methods to calculate the periodogram and estimate the period of a rhythmic time-course. Methods include Lomb-Scargle, fast Fourier transform, and three versions of the chi-square periodogram. See Tackenberg and Hughey (2021) <doi:10.1371/journal.pcbi.1008567>.

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2.70 score 1 stars 2 scripts 198 downloads