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smallRNA

Description Components related to miRNAs, ncRNAs, and the processing and analysis of small size-selected sequenced reads (less than 2kb).
Child categories
Novel smallRNA NovelMatureSeq NCRNAAnnot NovelExprMatrix NovelMirnas
Component Version Inputs Outputs Description
AnnotEnsembl 1.0 annot Takes the ncRNA fasta file downloaded from Ensembl and creates a gff file with the transcript IDs as the reference chromosome.
AnnotMirbase 1.0 annot Takes a GFF3 file downloaded from miRBase and modifies the genomic locations to reference by Ensembl transcript ID (instead of chromosome) and relative positions inside the transcript ID (start and end positions).
Bam2Fastq 0.1 in out Revert BAM file to Fastq file for realignment.
CreateSQLiteDB 0.1 DBlist Create miRNA-target gene database(s) for fast and simple SQLite query of potentially interesting regulatory pairs.
CreateSQLiteIDs 0.1 geneList wIDs For a subset of genes, create a file with additional reference IDs.
DataOverlap 1.0 annot1, annot2 annot Take the union of and collapse 2 datasets, with the option to filter out rows with NAs.
DEan 0.4 expr, treatment array, diffExpr Performs differential expression analyses in R between pairs of sample groups using up to 4 methods: DESeq, DESeq2, EdgeR, and upper-quartile normalization with t-test.
ExpressionStats 0.1 expr, ref, geneSet, bodyMap stats, statsArray, report Given an expression matrix and a CSV containing sample IDs and treatment groups, calculate basic statistics by treatment group: mean, median, and standard deviation of genes.
ExpressionSubset 0.1 exprMatrix, reference subset Given an expression matrix and a CSV containing a subset of interest in one column (e.g.
ExtractCond 0.1 exprMatrix, reference table Creates a custom input file defining treatment groups for MDSPlot component using expression matrices and a reference file.
GetUtrSeq 1.0 transcripts, connection UTR5, UTR3 Fetch UTR sequences of query transcripts.
GlobalCorrelation 1.2 gene, mirna correlated_filtered, correlated_all, expression_miRNA, expression_mRNA Compute correlation between miRNA and gene/transcript expression.
MirMatch 1.0 utrSeeds, matureSeq, pairs matched String match for between mature miRNA seeds and target UTR seeds.
SmallRNAPrep 1.0 reads fastq, stats Uses FASTX-Toolkit to perform adapter trimming, artifact filtering, base-quality filtering, and read trimming for single-end read data.
SmallRNAQC 1.0 reads, mates, stats, bam, mergeStats qc, report, fastqc Performs all 3 quality filtering steps (preprocessing, alignment to genome, and optional alignment to transcripts) in the smallRNA pipelines.
TPquery 0.3 refTable array, annot Retrieve target prediction and target validated data from an SQLite database to annotate a list of miRNAs or a list of miRNA-target gene pairs.
UtrSeq2Seeds 1.0 utrseq seeds Generate seeds with 15bp (XXXXXXXQXXXXXXX) with each query loci in middle.

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