{ "_id": "6a17e33eacfb0bcc41d9fefb", "Package": "DECIPHER", "Type": "Package", "Title": "Tools for curating, analyzing, and manipulating biological\nsequences", "Version": "3.9.0", "Date": "2026-04-27", "Author": "Erik Wright", "Maintainer": "Erik Wright ", "biocViews": "Clustering, Genetics, Sequencing, DataImport, Visualization,\nMicroarray, QualityControl, qPCR, Alignment, WholeGenome,\nMicrobiome, ImmunoOncology, GenePrediction, Phylogenetics,\nComparativeGenomics", "Description": "A toolset for deciphering and managing biological\nsequences.", "License": "GPL-3", "ByteCompile": "true", "URL": "http://DECIPHER.codes", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:35:55 UTC", "RemoteUrl": "https://github.com/bioc/DECIPHER", "RemoteRef": "HEAD", "RemoteSha": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-28 06:23:33 UTC", "User": "root" }, "MD5sum": "72cf693634156d8eb1113cd88bf52770", "_user": "bioc", "_type": "src", "_file": "DECIPHER_3.9.0.tar.gz", "_fileid": "62ec0e925d51d9246ad6efa450c8b5a8577f2a12fdc6593beb1baa429c03dd19", "_filesize": 19502858, "_sha256": "62ec0e925d51d9246ad6efa450c8b5a8577f2a12fdc6593beb1baa429c03dd19", "_created": "2026-05-28T06:23:33.000Z", "_published": "2026-05-28T06:39:58.488Z", "_jobs": [ { "job": 78235650376, "time": 207, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7259127958" }, { "job": 78235650420, "time": 772, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7259267999" }, { "job": 78235650467, "time": 898, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7259299383" }, { "job": 78235650448, "time": 742, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7259260687" }, { "job": 78235650438, "time": 870, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7259292630" }, { "job": 78235650409, "time": 626, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7259243006" }, { "job": 78235650415, "time": 648, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "7259246453" }, { "job": 78235650435, "time": 711, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7259264249" }, { "job": 78235650434, "time": 485, "config": "macos-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7259208231" }, { "job": 78233781666, "time": 965, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7259078444" }, { "job": 78235650402, "time": 122, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7259107802" }, { "job": 78235650405, "time": 455, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7259187885" }, { "job": 78235650421, "time": 310, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7259151912" }, { "job": 78235650391, "time": 451, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7259187220" } ], "_bioccheck": { "error": 2, "warning": 4, "note": 21 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/DECIPHER", "_commit": { "id": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379755 }, "_maintainer": { "name": "Erik Wright", "email": "erik.wright@bcm.edu", "login": "digitalwright", "description": "", "uuid": 6781840 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Biostrings", "version": ">= 2.59.1", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "Biostrings", "role": "LinkingTo" }, { "package": "S4Vectors", "role": "LinkingTo" }, { "package": "IRanges", "role": "LinkingTo" }, { "package": "XVector", "role": "LinkingTo" }, { "package": "methods", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "XVector", "role": "Imports" }, { "package": "RSQLite", "version": ">= 1.1", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 21, "_updates": [ { "week": "2025-42", "n": 1 }, { "week": "2025-43", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-12", "n": 1 }, { "week": "2026-18", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "3.9.0", "bioc": "3.24" }, { "branch": "release", "version": "3.8.0", "bioc": "3.23" } ], "_topics": [ "clustering", "genetics", "sequencing", "dataimport", "visualization", "microarray", "qualitycontrol", "qpcr", "alignment", "wholegenome", "microbiome", "immunooncology", "geneprediction", "phylogenetics", "comparativegenomics", "openmp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 5390, "source": "https://www.bioconductor.org/packages/stats/bioc/DECIPHER" }, "_mentions": 415, "_searchresults": 1468, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DECIPHER.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "AA_REDUCED", "Add2DB", "AdjustAlignment", "AlignDB", "AlignPairs", "AlignProfiles", "AlignSeqs", "AlignSynteny", "AlignTranslation", "AmplifyDNA", "Array2Matrix", "BrowseDB", "BrowseSeqs", "CalculateEfficiencyArray", "CalculateEfficiencyFISH", "CalculateEfficiencyPCR", "Clusterize", "Codec", "ConsensusSequence", "Cophenetic", "CorrectFrameshifts", "CreateChimeras", "DB2Seqs", "DesignArray", "DesignPrimers", "DesignProbes", "DesignSignatures", "DetectRepeats", "DigestDNA", "Disambiguate", "DistanceMatrix", "ExtractGenes", "FindChimeras", "FindGenes", "FindNonCoding", "FindSynteny", "FormGroups", "IdConsensus", "IdentifyByRank", "IdLengths", "IdTaxa", "IndexSeqs", "InferDemography", "InferRecombination", "InferSelection", "LearnNonCoding", "LearnTaxa", "MapCharacters", "MaskAlignment", "MeltDNA", "MODELS", "NNLS", "OrientNucleotides", "PredictDBN", "PredictHEC", "ReadDendrogram", "RemoveGaps", "ScoreAlignment", "SearchDB", "SearchIndex", "Seqs2DB", "StaggerAlignment", "TerminalChar", "TileSeqs", "Treeline", "TrimDNA", "WriteDendrogram", "WriteGenes", "Zipline" ], "_datasets": [ { "name": "BLOSUM", "title": "BLOSUM Amino Acid Substitution Matrices", "object": "BLOSUM", "file": "BLOSUM.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "deltaGrules", "title": "Free Energy of Hybridization of Probe/Target Quadruplets on Microarrays", "object": "deltaGrules", "file": "deltaGrules.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "deltaGrulesRNA", "title": "Pseudoenergy Parameters for RNA Quadruplets", "object": "deltaGrulesRNA", "file": "deltaGrulesRNA.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "deltaHrules", "title": "Change in Enthalpy of Hybridization of DNA/DNA Quadruplets in Solution", "object": "deltaHrules", "file": "deltaHrules.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "deltaHrulesRNA", "title": "Change in Enthalpy of Hybridization of RNA/RNA Quadruplets in Solution", "object": "deltaHrulesRNA", "file": "deltaHrulesRNA.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "deltaSrules", "title": "Change in Entropy of Hybridization of DNA/DNA Quadruplets in Solution", "object": "deltaSrules", "file": "deltaSrules.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "deltaSrulesRNA", "title": "Change in Entropy of Hybridization of RNA/RNA Quadruplets in Solution", "object": "deltaSrulesRNA", "file": "deltaSrulesRNA.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "HEC_MI1", "title": "Mutual Information for Protein Secondary Structure Prediction", "object": "HEC_MI1", "file": "HEC_MI1.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "HEC_MI2", "title": "Mutual Information for Protein Secondary Structure Prediction", "object": "HEC_MI2", "file": "HEC_MI2.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "MIQS", "title": "MIQS Amino Acid Substitution Matrix", "object": "MIQS", "file": "MIQS.RData", "class": [ "matrix", "array" ], "fields": [ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "J", "Z", "X", "*" ], "rows": 25, "table": true, "tojson": true }, { "name": "MMLSUM", "title": "MMLSUM Amino Acid Substitution Matrices", "object": "MMLSUM", "file": "MMLSUM.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "NonCodingRNA_Archaea", "title": "NonCoding Models for Common Non-Coding RNA Families", "object": "NonCodingRNA_Archaea", "file": "NonCodingRNA_Archaea.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "NonCodingRNA_Bacteria", "title": "NonCoding Models for Common Non-Coding RNA Families", "object": "NonCodingRNA_Bacteria", "file": "NonCodingRNA_Bacteria.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "NonCodingRNA_Eukarya", "title": "NonCoding Models for Common Non-Coding RNA Families", "object": "NonCodingRNA_Eukarya", "file": "NonCodingRNA_Eukarya.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "PAM", "title": "PAM Amino Acid Substitution Matrices", "object": "PAM", "file": "PAM.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "PFASUM", "title": "PFASUM Amino Acid Substitution Matrices", "object": "PFASUM", "file": "PFASUM.RData", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "RESTRICTION_ENZYMES", "title": "Common Restriction Enzyme's Cut Sites", "object": "RESTRICTION_ENZYMES", "file": "RESTRICTION_ENZYMES.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "TrainingSet_16S", "title": "Training Set for Classification of 16S rRNA Gene Sequences", "object": "TrainingSet_16S", "file": "TrainingSet_16S.RData", "class": [ "Taxa", "Train" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "DECIPHER-package", "title": "Tools for curating, analyzing, and manipulating biological sequences", "topics": [ "DECIPHER-package", "DECIPHER" ] }, { "page": "AA_REDUCED", "title": "Reduced amino acid alphabets", "topics": [ "AA_REDUCED" ] }, { "page": "Add2DB", "title": "Add Data to a Database", "topics": [ "Add2DB" ] }, { "page": "AdjustAlignment", "title": "Improve An Existing Alignment By Adjusting Gap Placements", "topics": [ "AdjustAlignment" ] }, { "page": "AlignDB", "title": "Align Two Sets of Aligned Sequences in a Sequence Database", "topics": [ "AlignDB" ] }, { "page": "AlignPairs", "title": "Align pairs of sequences", "topics": [ "AlignPairs" ] }, { "page": "AlignProfiles", "title": "Align Two Sets of Aligned Sequences", "topics": [ "AlignProfiles" ] }, { "page": "AlignSeqs", "title": "Align a Set of Unaligned Sequences", "topics": [ "AlignSeqs" ] }, { "page": "AlignSynteny", "title": "Pairwise Aligns Syntenic Blocks", "topics": [ "AlignSynteny" ] }, { "page": "AlignTranslation", "title": "Align Sequences By Their Amino Acid Translation", "topics": [ "AlignTranslation" ] }, { "page": "AmplifyDNA", "title": "Simulate Amplification of DNA by PCR", "topics": [ "AmplifyDNA" ] }, { "page": "Array2Matrix", "title": "Create a Matrix Representation of a Microarray", "topics": [ "Array2Matrix" ] }, { "page": "BLOSUM", "title": "BLOSUM Amino Acid Substitution Matrices", "topics": [ "BLOSUM" ] }, { "page": "BrowseDB", "title": "View a Database Table in a Web Browser", "topics": [ "BrowseDB" ] }, { "page": "BrowseSeqs", "title": "View Sequences in a Web Browser", "topics": [ "BrowseSeqs" ] }, { "page": "CalculateEfficiencyArray", "title": "Predict the Hybridization Efficiency of Probe/Target Sequence Pairs", "topics": [ "CalculateEfficiencyArray" ] }, { "page": "CalculateEfficiencyFISH", "title": "Predict Thermodynamic Parameters of Probe/Target Sequence Pairs", "topics": [ "CalculateEfficiencyFISH" ] }, { "page": "CalculateEfficiencyPCR", "title": "Predict Amplification Efficiency of Primer Sequences", "topics": [ "CalculateEfficiencyPCR" ] }, { "page": "Clusterize", "title": "Cluster Sequences By Distance", "topics": [ "Clusterize" ] }, { "page": "Codec", "title": "Compression/Decompression of Character Vectors", "topics": [ "Codec" ] }, { "page": "ConsensusSequence", "title": "Create a Consensus Sequence", "topics": [ "ConsensusSequence" ] }, { "page": "Cophenetic", "title": "Compute cophenetic distances on dendrogram objects", "topics": [ "Cophenetic" ] }, { "page": "CorrectFrameshifts", "title": "Corrects Frameshift Errors In Protein Coding Sequences", "topics": [ "CorrectFrameshifts" ] }, { "page": "CreateChimeras", "title": "Create Artificial Chimeras", "topics": [ "CreateChimeras" ] }, { "page": "DB2Seqs", "title": "Export Database Sequences to a FASTA or FASTQ File", "topics": [ "DB2Seqs" ] }, { "page": "deltaGrules", "title": "Free Energy of Hybridization of Probe/Target Quadruplets on Microarrays", "topics": [ "deltaGrules" ] }, { "page": "deltaGrulesRNA", "title": "Pseudoenergy Parameters for RNA Quadruplets", "topics": [ "deltaGrulesRNA" ] }, { "page": "deltaHrules", "title": "Change in Enthalpy of Hybridization of DNA/DNA Quadruplets in Solution", "topics": [ "deltaHrules" ] }, { "page": "deltaHrulesRNA", "title": "Change in Enthalpy of Hybridization of RNA/RNA Quadruplets in Solution", "topics": [ "deltaHrulesRNA" ] }, { "page": "deltaSrules", "title": "Change in Entropy of Hybridization of DNA/DNA Quadruplets in Solution", "topics": [ "deltaSrules" ] }, { "page": "deltaSrulesRNA", "title": "Change in Entropy of Hybridization of RNA/RNA Quadruplets in Solution", "topics": [ "deltaSrulesRNA" ] }, { "page": "DesignArray", "title": "Design a Set of DNA Microarray Probes for Detecting Sequences", "topics": [ "DesignArray" ] }, { "page": "DesignPrimers", "title": "Design PCR Primers Targeting a Specific Group of Sequences", "topics": [ "DesignPrimers" ] }, { "page": "DesignProbes", "title": "Design FISH Probes Targeting a Specific Group of Sequences", "topics": [ "DesignProbes" ] }, { "page": "DesignSignatures", "title": "Design PCR Primers for Amplifying Group-Specific Signatures", "topics": [ "DesignSignatures" ] }, { "page": "DetectRepeats", "title": "Detect Repeats in a Sequence", "topics": [ "DetectRepeats" ] }, { "page": "DigestDNA", "title": "Simulate Restriction Digestion of DNA", "topics": [ "DigestDNA" ] }, { "page": "Disambiguate", "title": "Expand Ambiguities into All Permutations of a DNAStringSet", "topics": [ "Disambiguate" ] }, { "page": "DistanceMatrix", "title": "Calculate the Distances Between Sequences", "topics": [ "DistanceMatrix" ] }, { "page": "ExtractGenes", "title": "Extract Predicted Genes from a Genome", "topics": [ "ExtractGenes" ] }, { "page": "FindChimeras", "title": "Find Chimeras in a Sequence Database", "topics": [ "FindChimeras" ] }, { "page": "FindGenes", "title": "Find Genes in a Genome", "topics": [ "FindGenes" ] }, { "page": "FindNonCoding", "title": "Find Non-Coding RNAs in a Genome", "topics": [ "FindNonCoding" ] }, { "page": "FindSynteny", "title": "Finds Synteny in a Sequence Database", "topics": [ "FindSynteny" ] }, { "page": "FormGroups", "title": "Forms Groups By Rank", "topics": [ "FormGroups" ] }, { "page": "Genes-class", "title": "Genes objects and accessors", "topics": [ "Genes-class", "plot.Genes", "print.Genes", "[.Genes" ] }, { "page": "HEC_MI", "title": "Mutual Information for Protein Secondary Structure Prediction", "topics": [ "HEC_MI1", "HEC_MI2" ] }, { "page": "IdConsensus", "title": "Create Consensus Sequences by Groups", "topics": [ "IdConsensus" ] }, { "page": "IdentifyByRank", "title": "Identify By Taxonomic Rank", "topics": [ "IdentifyByRank" ] }, { "page": "IdLengths", "title": "Determine the Number of Characters in Each Sequence", "topics": [ "IdLengths" ] }, { "page": "IdTaxa", "title": "Assign Sequences a Taxonomic Classification", "topics": [ "IdTaxa" ] }, { "page": "IndexSeqs", "title": "Build an inverted index", "topics": [ "IndexSeqs" ] }, { "page": "InferDemography", "title": "Infer Demographic History from Allele Frequencies", "topics": [ "InferDemography" ] }, { "page": "InferRecombination", "title": "Infer Recombination Parameters from Correlation Profiles", "topics": [ "InferRecombination" ] }, { "page": "InferSelection", "title": "Infer Codon Selection on Protein Coding Sequences", "topics": [ "InferSelection" ] }, { "page": "InvertedIndex-class", "title": "InvertedIndex objects", "topics": [ "InvertedIndex-class", "print.InvertedIndex" ] }, { "page": "LearnNonCoding", "title": "Learn a Non-Coding RNA Model", "topics": [ "LearnNonCoding" ] }, { "page": "LearnTaxa", "title": "Train a Classifier for Assigning Taxonomy", "topics": [ "LearnTaxa" ] }, { "page": "MapCharacters", "title": "Map Changes in Ancestral Character States", "topics": [ "MapCharacters" ] }, { "page": "MaskAlignment", "title": "Mask Highly Variable Regions of An Alignment", "topics": [ "MaskAlignment" ] }, { "page": "MeltDNA", "title": "Simulate Melting of DNA", "topics": [ "MeltDNA" ] }, { "page": "MIQS", "title": "MIQS Amino Acid Substitution Matrix", "topics": [ "MIQS" ] }, { "page": "MMLSUM", "title": "MMLSUM Amino Acid Substitution Matrices", "topics": [ "MMLSUM" ] }, { "page": "MODELS", "title": "Available Models of Sequence Evolution", "topics": [ "MODELS" ] }, { "page": "NNLS", "title": "Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem", "topics": [ "NNLS" ] }, { "page": "NonCoding-class", "title": "NonCoding Objects and Methods", "topics": [ "NonCoding-class", "print.NonCoding" ] }, { "page": "NonCodingRNA", "title": "NonCoding Models for Common Non-Coding RNA Families", "topics": [ "NonCodingRNA_Archaea", "NonCodingRNA_Bacteria", "NonCodingRNA_Eukarya" ] }, { "page": "OrientNucleotides", "title": "Orient Nucleotide Sequences", "topics": [ "OrientNucleotides" ] }, { "page": "PAM", "title": "PAM Amino Acid Substitution Matrices", "topics": [ "PAM" ] }, { "page": "PFASUM", "title": "PFASUM Amino Acid Substitution Matrices", "topics": [ "PFASUM" ] }, { "page": "PredictDBN", "title": "Predict RNA Secondary Structure in Dot-Bracket Notation", "topics": [ "PredictDBN" ] }, { "page": "PredictHEC", "title": "Predict Protein Secondary Structure", "topics": [ "PredictHEC" ] }, { "page": "ReadDendrogram", "title": "Read a Dendrogram from a Newick Formatted File", "topics": [ "ReadDendrogram" ] }, { "page": "RemoveGaps", "title": "Remove Gap Characters in Sequences", "topics": [ "RemoveGaps" ] }, { "page": "RESTRICTION_ENZYMES", "title": "Common Restriction Enzyme's Cut Sites", "topics": [ "RESTRICTION_ENZYMES" ] }, { "page": "ScoreAlignment", "title": "Score a Multiple Sequence Alignment", "topics": [ "ScoreAlignment" ] }, { "page": "SearchDB", "title": "Obtain Specific Sequences from a Database", "topics": [ "SearchDB" ] }, { "page": "SearchIndex", "title": "Search an inverted index", "topics": [ "SearchIndex" ] }, { "page": "Seqs2DB", "title": "Add Sequences from Text File to Database", "topics": [ "Seqs2DB" ] }, { "page": "StaggerAlignment", "title": "Produce a Staggered Alignment", "topics": [ "StaggerAlignment" ] }, { "page": "Synteny-class", "title": "Synteny blocks and hits", "topics": [ "as.dist.Synteny", "pairs.Synteny", "plot.Synteny", "print.Synteny", "Synteny-class", "[.Synteny" ] }, { "page": "Taxa-class", "title": "Taxa training and testing objects", "topics": [ "c.Taxa", "plot.Taxa", "print.Taxa", "Taxa-class", "[.Taxa" ] }, { "page": "TerminalChar", "title": "Determine the Number of Terminal Characters", "topics": [ "TerminalChar" ] }, { "page": "TileSeqs", "title": "Form a Set of Tiles for Each Group of Sequences.", "topics": [ "TileSeqs" ] }, { "page": "TrainingSet_16S", "title": "Training Set for Classification of 16S rRNA Gene Sequences", "topics": [ "TrainingSet_16S" ] }, { "page": "Treeline", "title": "Construct a Phylogenetic Tree", "topics": [ "TreeLine", "Treeline" ] }, { "page": "TrimDNA", "title": "Trims DNA Sequences to the High Quality Region Between Patterns", "topics": [ "TrimDNA" ] }, { "page": "WriteDendrogram", "title": "Write a Dendrogram to Newick Format", "topics": [ "WriteDendrogram" ] }, { "page": "WriteGenes", "title": "Write Genes to a File", "topics": [ "WriteGenes" ] }, { "page": "Zipline", "title": "Summarize Multiple Phylogenetic Trees", "topics": [ "Zipline" ] } ], "_rundeps": [ "BiocGenerics", "Biostrings", "crayon", "DBI", "generics", "IRanges", "S4Vectors", "Seqinfo", "XVector" ], "_sysdeps": [ { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "ClassifySequences.Rnw", "filename": "ClassifySequences.pdf", "title": "Classify Sequences in R", "engine": "utils::Sweave", "headings": [], "created": "2017-10-24 11:07:56", "modified": "2025-04-03 23:36:39", "commits": 12 }, { "source": "DesignProbes.Rnw", "filename": "DesignProbes.pdf", "title": "Design Group-Specific FISH Probes in R", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:21:30", "modified": "2025-04-03 23:36:39", "commits": 16 }, { "source": "DesignPrimers.Rnw", "filename": "DesignPrimers.pdf", "title": "Design Group-Specific Primers in R", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:21:30", "modified": "2025-04-03 23:36:39", "commits": 15 }, { "source": "DesignMicroarray.Rnw", "filename": "DesignMicroarray.pdf", "title": "Design Microarray Probes in R", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:21:30", "modified": "2025-04-03 23:36:39", "commits": 13 }, { "source": "DesignSignatures.Rnw", "filename": "DesignSignatures.pdf", "title": "Design Primers that Yield Group-Specific Signatures", "engine": "utils::Sweave", "headings": [], "created": "2015-09-23 18:06:49", "modified": "2024-12-20 00:24:17", "commits": 10 }, { "source": "RepeatRepeat.Rnw", "filename": "RepeatRepeat.pdf", "title": "Detecting Obscure Tandem Repeats in Sequences", "engine": "utils::Sweave", "headings": [], "created": "2022-04-25 14:45:06", "modified": "2025-04-03 23:36:39", "commits": 11 }, { "source": "FindChimeras.Rnw", "filename": "FindChimeras.pdf", "title": "Finding Chimeric Sequences in R", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:21:30", "modified": "2025-04-03 23:36:39", "commits": 13 }, { "source": "DECIPHERing.Rnw", "filename": "DECIPHERing.pdf", "title": "Getting Started DECIPHERing", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:21:30", "modified": "2025-10-14 17:09:52", "commits": 34 }, { "source": "GrowingTrees.Rnw", "filename": "GrowingTrees.pdf", "title": "Growing Phylogenetic Trees in R with Treeline", "engine": "utils::Sweave", "headings": [], "created": "2022-04-25 14:45:06", "modified": "2026-04-27 23:57:29", "commits": 14 }, { "source": "PopulationGenetics.Rnw", "filename": "PopulationGenetics.pdf", "title": "Population Genetics Inference in R", "engine": "utils::Sweave", "headings": [], "created": "2025-04-03 23:36:39", "modified": "2026-03-22 12:58:53", "commits": 4 }, { "source": "SearchForResearch.Rnw", "filename": "SearchForResearch.pdf", "title": "Searching Biological Sequences for Research", "engine": "utils::Sweave", "headings": [], "created": "2024-02-11 18:41:50", "modified": "2025-04-07 21:26:40", "commits": 8 }, { "source": "ArtOfAlignmentInR.Rnw", "filename": "ArtOfAlignmentInR.pdf", "title": "The Art of Multiple Sequence Alignment in R", "engine": "utils::Sweave", "headings": [], "created": "2014-01-26 00:42:15", "modified": "2024-04-29 16:23:07", "commits": 24 }, { "source": "FindingNonCodingRNAs.Rnw", "filename": "FindingNonCodingRNAs.pdf", "title": "The Double Life of RNA: Uncovering Non-Coding RNAs", "engine": "utils::Sweave", "headings": [], "created": "2021-02-13 15:58:26", "modified": "2024-11-29 20:42:57", "commits": 5 }, { "source": "FindingGenes.Rnw", "filename": "FindingGenes.pdf", "title": "The Magic of Gene Finding", "engine": "utils::Sweave", "headings": [], "created": "2020-10-26 21:58:10", "modified": "2024-01-17 12:54:02", "commits": 8 }, { "source": "ClusteringSequences.Rnw", "filename": "ClusteringSequences.pdf", "title": "Upsize Your Clustering with Clusterize", "engine": "utils::Sweave", "headings": [], "created": "2022-09-15 21:16:53", "modified": "2025-03-08 19:57:42", "commits": 10 } ], "_score": 10.572716633612073, "_indexed": true, "_nocasepkg": "decipher", "_universes": [ "bioc", "digitalwright" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.9.0", "date": "2026-05-28T06:26:33.000Z", "distro": "noble", "arch": "aarch64", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "1f182cdab94bfe8a8e0af4777ff2fb94d528f6cff3c9f97bdef2fd8409acc441", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" }, { "r": "4.7.0", "os": "linux", "version": "3.9.0", "date": "2026-05-28T06:27:44.000Z", "distro": "noble", "arch": "x86_64", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "558ad084c8a376623dd8cac70f424460849779d8380e72a80ae9b4ee123fb878", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" }, { "r": "4.6.0", "os": "linux", "version": "3.9.0", "date": "2026-05-28T06:26:29.000Z", "distro": "noble", "arch": "aarch64", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "a7687157b1e3ff549723200f6e640b24dc68a068430b196d77e156898b314fd6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" }, { "r": "4.6.0", "os": "linux", "version": "3.9.0", "date": "2026-05-28T06:27:18.000Z", "distro": "noble", "arch": "x86_64", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "3bac8f5bf008d567eafd3d8464578a6471555ab7c1137aec972e97ea01c21a5e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" }, { "r": "4.5.3", "os": "mac", "version": "3.9.0", "date": "2026-05-28T06:26:55.000Z", "arch": "aarch64", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "935232e3466d5c661044663b7e0fcb9e2aa02d1f5f10d61bd85ebb8d73be473b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" }, { "r": "4.5.3", "os": "mac", "version": "3.9.0", "date": "2026-05-28T06:28:48.000Z", "arch": "x86_64", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "ac996acaa4b903be96d424ce808b09b77edc58f3f213018ed641f8856bc92d28", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" }, { "r": "4.6.0", "os": "mac", "version": "3.9.0", "date": "2026-05-28T06:27:09.000Z", "arch": "aarch64", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "45f5c78628a5e602abcceac7e3ac38edffa794376ba097750314eb83ecf7fc13", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" }, { "r": "4.6.0", "os": "mac", "version": "3.9.0", "date": "2026-05-28T06:27:44.000Z", "arch": "x86_64", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "a1c3e89c83feb4410eca822ad23c51486e0f7879e5ec7725e3819f384ac2e398", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" }, { "r": "4.6.0", "os": "wasm", "version": "3.9.0", "date": "2026-05-28T06:26:30.000Z", "arch": "emscripten", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "f5873b3da4975f2e502b5cb99cfef7210adb8d9170bf6e522e35f74a4bb2a4e9", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" }, { "r": "4.7.0", "os": "win", "version": "3.9.0", "date": "2026-05-28T06:25:36.000Z", "arch": "x86_64", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "bbd92973470cad9bc32e67d66becf8ac7bb636f86b246f202d7c1d8dab2fe46c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" }, { "r": "4.5.3", "os": "win", "version": "3.9.0", "date": "2026-05-28T06:25:42.000Z", "arch": "x86_64", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "bc002fa1311c614af5c7e8007688b9ecff62f2592c0de13a5fd7d962eb662a0b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" }, { "r": "4.6.0", "os": "win", "version": "3.9.0", "date": "2026-05-28T06:25:42.000Z", "arch": "x86_64", "commit": "fe1126ce1b8ab378f37eec12b643977b95d748e6", "fileid": "c0d56ada24f90a18f22009423cf9e5fed6c6da813af59537d2b22248eae5cf34", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26557935021" } ] }