PWMEnrich - PWM enrichment analysis
A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.
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motifannotationsequencematchingsoftware
5.25 score 89 scripts 752 downloadsrTRM - Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks
rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.
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transcriptionnetworkgeneregulationgraphandnetworkbioconductorbioinformatics
4.86 score 3 stars 1 dependents 5 scripts 616 downloadscodelink - Manipulation of Codelink microarray data
This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.
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microarrayonechanneldataimportpreprocessing
4.20 score 10 scripts 769 downloadsrTRMui - A shiny user interface for rTRM
This package provides a web interface to compute transcriptional regulatory modules with rTRM.
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transcriptionnetworkgeneregulationgraphandnetworkgui
3.30 score 1 stars 3 scripts 456 downloadsPWMEnrich.Hsapiens.background - H. sapiens background for PWMEnrich
PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs.
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homo_sapiens_datacghdatadatapkg
2.82 score 33 scriptsPWMEnrich.Dmelanogaster.background - D. melanogaster background for PWMEnrich
PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs.
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drosophila_melanogaster_datadatapkg
2.34 score 11 scriptsPWMEnrich.Mmusculus.background - M. musculus background for PWMEnrich
PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs.
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mus_musculus_datadatapkg
2.30 score 4 scripts