{ "_id": "6ac28d8ad743750d376d8c3f", "Package": "seqpac", "Type": "Package", "Title": "Seqpac: A Framework for smallRNA analysis in R using\nSequence-Based Counts", "Version": "1.12.0", "Authors@R": "c(\nperson(\"Signe\", \"Isacson\", email=\"signe.skog@liu.se\", role= c(\"aut\", \"ctb\")),\nperson(\"Daniel\", \"Natt\", email=\"daniel.natt@liu.se\", role= c(\"aut\", \"fnd\")),\nperson(\"Lovisa\", \"Örkenby\", email=\"lovisa.orkenby@liu.se\", role= c(\"aut\", \"ctb\")),\nperson(\"Alessandro\", \"Gozzo\", email=\"alessandro.gozzo@liu.se\", role= c(\"aut\",\"ctb\", \"cre\"),\ncomment=c(ORCID=\"0000-0002-6466-627X\")),\nperson(\"Anna\", \"Asratian\", email=\"anna.asratian@liu.se\", role= c(\"aut\", \"ctb\")),\nperson(\"Anita\", \"Öst\", email=\"anita.ost@liu.se\", role= c(\"aut\", \"fnd\"))\n)", "Description": "Seqpac provides functions and workflows for analysis of\nshort sequenced reads. It was originally developed for small\nRNA analysis, but can be implemented on any sequencing raw data\n(provided as a fastq-file), where the unit of measurement is\ncounts of unique sequences. The core of the seqpac workflow is\nthe generation and subsequence analysis/visualization of a\nstandardized object called PAC. Using an innovative targeting\nsystem, Seqpac process, analyze and visualize sample or\nsequence group differences using the PAC object. A PAC object\nin its most basic form is a list containing three types of data\nframes. - Phenotype table (P): Sample names (rows) with\nassociated metadata (columns) e.g. treatment. - Annotation\ntable (A): Unique sequences (rows) with annotation (columns),\neg. reference alignments. - Counts table (C): Counts of unique\nsequences (rows) for each sample (columns). The PAC-object\nfollows the rule: - Row names in P must be identical with\ncolumn names in C. - Row names in A must be identical with row\nnames in C. Thus P and A describes the columns and rows in C,\nrespectively. The targeting system, will either target specific\nsamples in P (pheno_target) or sequences in A (anno_target) and\ngroup them according to a target column in P and A,\nrespectively (see vignettes for more details).", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "URL": "https://github.com/Oestlab/seqpac", "BugReports": "https://github.com/OestLab/seqpac/issues", "biocViews": "Workflow, BasicWorkflow, GeneExpressionWorkflow,\nEpigeneticsWorkflow, AnnotationWorkflow", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libfreetype6-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:44:54 UTC", "RemoteUrl": "https://github.com/bioc/seqpac", "RemoteRef": "RELEASE_3_23", "RemoteSha": "32327358db6b9bfba00447e145fd26309278e7ba", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-04 17:16:39 UTC", "User": "root" }, "Author": "Signe Isacson [aut, ctb],\nDaniel Natt [aut, fnd],\nLovisa Örkenby [aut, ctb],\nAlessandro Gozzo [aut, ctb, cre] (ORCID:\n),\nAnna Asratian [aut, ctb],\nAnita Öst [aut, fnd]", "Maintainer": "Alessandro Gozzo ", "_user": "bioc-release", "_type": "src", "_file": "seqpac_1.12.0.tar.gz", "_fileid": "https://r2.ropensci.org/b01993ef11091d490ffb3925a32be1d5df0aba987778efa43e8fec0535f4498a", "_filesize": 3634266, "_sha256": "b01993ef11091d490ffb3925a32be1d5df0aba987778efa43e8fec0535f4498a", "_expires": "2027-01-12T17:31:52.000Z", "_created": "2026-10-04T17:16:39.000Z", "_published": "2026-10-07T14:20:45.856Z", "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219442957", "_status": "success", "_upstream": "https://github.com/bioc/seqpac", "_commit": { "id": "32327358db6b9bfba00447e145fd26309278e7ba", "author": "lshep ", "committer": "lshep ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380294 }, "_maintainer": { "name": "Alessandro Gozzo", "email": "alessandro.gozzo@liu.se", "orcid": "0000-0002-6466-627X" }, "_distro": "resolute", "_jobs": [ { "job": 111488013319, "time": 184, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11309891728" }, { "job": 111488013402, "time": 703, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11310032349" }, { "job": 111488013428, "time": 810, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11309399720" }, { "job": 111488013344, "time": 641, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11310178069" }, { "job": 111488013395, "time": 644, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11309678985" }, { "job": 111486672881, "time": 431, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11309886603" }, { "job": 111488013360, 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generation" ], "topics": [ "PAC_create" ] }, { "page": "PAC_deseq", "title": "A wrapper to DESeq2 that apply differential expression analysis on a PAC object", "concept": [ "PAC analysis" ], "topics": [ "PAC_deseq" ] }, { "page": "PAC_filter", "title": "Filter a PAC object on sequence size and coverage", "concept": [ "PAC analysis" ], "topics": [ "PAC_filter" ] }, { "page": "PAC_filtsep", "title": "Generates filtered sequence name list separated on group", "concept": [ "PAC analysis" ], "topics": [ "PAC_filtsep" ] }, { "page": "PAC_gtf", "title": "Annotate against a GTF file", "concept": [ "PAC analysis" ], "topics": [ "PAC_gtf" ] }, { "page": "PAC_jitter", "title": "Plots jitter plot from PAC object", "concept": [ "PAC analysis" ], "topics": [ "PAC_jitter" ] }, { "page": "PAC_mapper", "title": "Advanced sequence mapping of a PAC object", "concept": [ "PAC analysis" ], "topics": [ "PAC_mapper" ] }, { "page": "PAC_nbias", "title": "Generates a nucleotide bias analysis from a PAC object", "concept": [ "PAC analysis" ], "topics": [ "PAC_nbias" ] }, { "page": "PAC_norm", "title": "Generates normalized values from a PAC object", "concept": [ "PAC analysis" ], "topics": [ "PAC_norm" ] }, { "page": "PAC_pca", "title": "Principle component analysis with scatterplots from PAC", "concept": [ "PAC analysis" ], "topics": [ "PAC_pca" ] }, { "page": "PAC_pie", "title": "Pie plot from PAC", "concept": [ "PAC analysis" ], "topics": [ "PAC_pie" ] }, { "page": "PAC_saturation", "title": "Filter a PAC object on sequence size and coverage", "concept": [ "PAC analysis" ], "topics": [ "PAC_saturation" ] }, { "page": "PAC_sizedist", "title": "Generates size distribution plots from a PAC object", "concept": [ "PAC analysis" ], "topics": [ "PAC_sizedist" ] }, { "page": "PAC_stackbar", "title": "Plot stackbars from PAC", "concept": [ "PAC analysis" ], "topics": [ "PAC_stackbar" ] }, { "page": "PAC_summary", "title": "Summarizes PAC objects", "concept": [ "PAC analysis" ], "topics": [ 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trimmed fastq", "Optimizing for low-end systems and challenging data", "Outputs from make_counts", "Evidence filtering", "Generate the phenotype table (make_pheno)", "Generating the PAC object (make_PAC)", "Preprocessing the PAC object", "Targeting objects", "Filtering", "Extracts sequences with >=5 counts in 100% of samples within each stage", "Storage of processed data in PAC", "Normalization", "Generate annotations", "Quick guide of the annotation workflow", "Fasta references", "The reannotation workflow", "The functions in the reanno workflow", "Reannotation in action", "Genome mapping", "Path to your output folder", "or a temp folder", "Look up the your own Bowtie indexed reference genomes (fasta)", "For testing, you can use a small mycoplasma genome provided with Seqpac", "But remember to provide single genomes as a named list anyway.", "The name will be used to keep track of your genome.", "Output as separate table", "Output merged with provided PAC object", "Example of original reference name annotations", "Finished genome annotation", "Currently classification does not discriminate", "Set the hierarchy and remember that it is order sensitive.", "Here: S5_rRNA >> Other_rRNA >> mt:tRNA >> tRNA", "Remember to use 'regular expressions' if you wish to catch all:", "What happens if you don't catch all:", "No mismatch allowed using hierarchy_1", "Instead using hierarchy_2", "Note, setting 'merge_pac=FALSE' returns a one-column data.frame only", "containing the new hierarchical classifications.", "Lets increase number of mismatches an merge it with the PAC", "(How many mismatches depends on what you allowed previously in the workflow)", "Now we also have some mitochondrial tRNA", "Summarize data over groups (PAC_summary)", "Differential Expression using PAC object (PAC_deseq)", "Principal component analysis (PAC_pca)", "Size distribution and nucleotide bias", "Simple stacked bars and pie charts", "Specilized analysis in Seqpac", "Advanced alignment analysis (tRNA class analysis)", "tRNA analysis in Seqpac", "First create an annotation blank PAC with group means", "Then reannotate only tRNA using the PAC_mapper function", "or use the provided fasta", "map_object <- PAC_mapper(pac_trna, input=ref, N_up = \"NNN\", N_down = \"NNN\",", "mismatches=0, threads=1, report_string=TRUE,", "override=TRUE)", "Hint: By adding N_up ad N_down you can make sure that modified fragments (like", "3' -CAA in mature tRNA are included).", "Plot tRNA using xseq=TRUE gives you the reference sequence as X-axis:", "(OBS! Long reference will not show well.)", "Targeting a single tRNA using a summary data.frame", "Find tRNAs with many fragments", "1st extract number of rows from each alignment", "The test data is highly down an filterd sampled, but still some with tRNA have", "a few alignment", "Lets select a few of them and plot them", "Generate range types using a ss-file", "Download ss object from GtRNAdb", "(\"http://gtrnadb.ucsc.edu/\")", "or for testing use the provided ss-file in secpac", "Classify fragments according to loop cleavage (small loops are omitted)", "Remove reference tRNAs with no hits", "Now we have quite comprehensive tRNA loop annotations", "Don't forget to check ?map_rangetype to obtain more options", "Function classifying 5'-tRF, 5'halves, i-tRF, 3'-tRF, 3'halves", "Does all tRNAs have 3 loops?", "Set tolerance for classification as a terminal tRF", "Important:", "We set N_up and N_down to \"NNN\" in the PAC_mapper step. To make sure", "that we have a tolerance that include the original tRNA sequence", "we set terminal= 2+3 (5).", "Plot tRNA types", "Now use PAC_trna to generate some graphs based on grand means" ], "created": "2021-04-06 15:56:52", "modified": "2026-03-30 12:55:58", "commits": 22 } ], "_score": 4.732393759822968, "_indexed": false, "_nocasepkg": "seqpac", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/seqpac", "_progress_url": "https://github.com/r-universe/bioc-release/actions/runs/37635848374", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.12.0", "date": "2026-10-04T17:20:27.000Z", "distro": "resolute", "commit": "32327358db6b9bfba00447e145fd26309278e7ba", "fileid": "https://r2.ropensci.org/f1092845f5c273bd45a8aa7014df28fd053566ae56175f414bf47b2d4933baf6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219442957" }, { "r": "4.6.1", "os": "linux", "version": "1.12.0", "date": "2026-10-04T17:20:59.000Z", "distro": "resolute", "commit": "32327358db6b9bfba00447e145fd26309278e7ba", "fileid": "https://r2.ropensci.org/df054569ec55bed4d44aacade34c73bb0bd854ce01ae3ab0f5eb75acd70b44d0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219442957" }, { "r": "4.5.3", "os": "mac", "version": "1.12.0", "date": "2026-10-04T17:19:10.000Z", "commit": "32327358db6b9bfba00447e145fd26309278e7ba", "fileid": "https://r2.ropensci.org/ff53fa6e6bb2c1e4eebdb142a194e1afea1316cf38913e49cfc0649401374fe9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219442957" }, { "r": "4.6.1", "os": "mac", "version": "1.12.0", "date": "2026-10-04T17:18:48.000Z", "commit": "32327358db6b9bfba00447e145fd26309278e7ba", "fileid": "https://r2.ropensci.org/ca9aaa5b0d6bfc8f1adf892b1f80f4012cab6b0cc37ae5d922c2ddd8daf192fb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219442957" }, { "r": "4.6.0", "os": "wasm", "version": "1.12.0", "date": "2026-10-04T17:19:53.000Z", "commit": "32327358db6b9bfba00447e145fd26309278e7ba", "fileid": "https://r2.ropensci.org/2223ccb85c700278238feda604b0b3d5e7fd88d055aed1fef5e07a2f9d1645eb", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219442957" }, { "r": "4.7.0", "os": "win", "version": "1.12.0", "date": "2026-10-04T17:18:51.000Z", "commit": "32327358db6b9bfba00447e145fd26309278e7ba", "fileid": "https://r2.ropensci.org/fc9c87571f5967065e7406fbdc8b46a5f9bf92814b54da4b1d040ecc7084635a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219442957" }, { "r": "4.5.3", "os": "win", "version": "1.12.0", "date": "2026-10-04T17:18:35.000Z", "commit": "32327358db6b9bfba00447e145fd26309278e7ba", "fileid": "https://r2.ropensci.org/145229aea6c0b886ca9399470d8b47370d3fa9fc1249554b63391e220f4538b3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219442957" }, { "r": "4.6.1", "os": "win", "version": "1.12.0", "date": "2026-10-04T17:18:48.000Z", "commit": "32327358db6b9bfba00447e145fd26309278e7ba", "fileid": "https://r2.ropensci.org/1afd688392adb0b38a33081382e3b82b1c2c4f57d8e02b987d3e441b9c98a620", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37219442957" } ] }