TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It c
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("TFBSTools")toPWM and toICM.searchSeq or searchAln.getMatrixSet.permuteMatrix and rPWMDmm.seqLogo.motifmatchr instead, because searchSeq is optimized for targeted DNAString or DNAStringSet objects rather than massive GRanges peak sets.universalmotif because runMEME requires the external MEME suite to be installed on the system.PFMatrix objects, DNAString or DNAStringSet for sequences, and Axt objects for alignments.toPWM (e.g., "log2probratio") or the type of p-value calculation in pvalues (e.g., "TFMPvalue").toPWM.c(A=0.25, C=0.25, G=0.25, T=0.25)).searchSeq or searchAln.toICM indicating whether to apply the Schneider correction.searchSeq (e.g., "*" for both strands).pseudocounts=0.8 in toPWM rather than the square root of sequences to avoid overly harsh corrections on zero values.searchSeq, use pvalues with type="TFMPvalue" to calculate empirical p-values for the match scores.writeGFF3 or writeGFF2 to export SiteSet objects into standard genomic formats for downstream visualization.runMEME fails to execute.binary argument correctly points to the executable.searchSeq returns too many false positive hits.min.score threshold (e.g., from "60%" to "90%") to enforce stricter matching.toPWM throws an error due to zero counts.pseudocounts is set to a positive value (like 0.8) to eliminate zero values before log transformation.GRanges objects.matchPWM), though it lacks the advanced statistical models and TFFM support of TFBSTools.This skill is the knowledge layer — when, why, and how to use tfbstools. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.
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The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
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This tool uses the label-tree function from HyPhy to annotate a phylogenetic tree. It allows users to select a subset of leaves using either a regular expression or a list of sequence names, and then apply a specified label to these selecte
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This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, En
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apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
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ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).
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AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched with
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