• iMiRNA-PseDPC

  • Referenced in 10 articles [sw22425]
  • iMiRNA-PseDPC: microRNA precursor identification with a pseudo distance-pair composition approach. A microRNA (miRNA...
  • starBase

  • Referenced in 10 articles [sw23121]
  • from large-scale CLIP-Seq data. Although microRNAs (miRNAs), other non-coding RNAs (ncRNAs...
  • miRecords

  • Referenced in 6 articles [sw29356]
  • miRecords: an integrated resource for microRNA–target interactions. MicroRNAs (miRNAs) are an important class...
  • EXPANDER

  • Referenced in 8 articles [sw30158]
  • categories; TF binding sites in promoter regions; MicroRNA sites in 3’-UTRs and; Biological pathways...
  • miTarget

  • Referenced in 4 articles [sw27473]
  • miTarget: microRNA target gene prediction using a support vector machine. Background: MicroRNAs (miRNAs) are small...
  • TopKLists

  • Referenced in 5 articles [sw13900]
  • usefulness of the package, we integrated microRNA data of non-small cell lung cancer across...
  • MiPred

  • Referenced in 5 articles [sw29580]
  • MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined...
  • miRanalyzer

  • Referenced in 2 articles [sw29579]
  • miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Next-generation sequencing ... these data, miRanalyzer (i) detects all known microRNA sequences annotated in miRBase, (ii) finds ... transcribed sequences and (iii) predicts new microRNAs. The prediction of new microRNAs is an especially ... many species with very few known microRNAs. Therefore, we implemented a highly accurate machine learning...
  • MiRFinder

  • Referenced in 3 articles [sw29577]
  • software implementation for genome-wide fast microRNA precursor scans. Background: MicroRNAs (miRNAs) are recognized...
  • ProMiR II

  • Referenced in 3 articles [sw29582]
  • prediction of clustered, nonclustered, conserved and nonconserved microRNAs. ProMiR is a web-based service ... prediction of potential microRNAs (miRNAs) in a query sequence of 60–150 nt, using...
  • miRTarBase

  • Referenced in 4 articles [sw29360]
  • experimentally validated miRNA-target interactions database. MicroRNAs (miRNAs) are small non-coding RNAs of approximately...
  • TargetSpy

  • Referenced in 2 articles [sw29586]
  • TargetSpy: a supervised machine learning approach for microRNA target prediction. Results: We developed TargetSpy ... change in protein production for five selected microRNAs our method shows superior performance ... target sites without a seed match per microRNA that are missed by all other currently...
  • mirTools

  • Referenced in 2 articles [sw29588]
  • mirTools: microRNA profiling and discovery based on high-throughput sequencing. miRNAs are small, non-coding ... approaches in mirTools will greatly facilitate current microRNA researches in multiple ways. mirTools...
  • mirWIP

  • Referenced in 1 article [sw27474]
  • mirWIP: microRNA Target Prediction Based on miRNP Enriched Transcripts. Target prediction for animal microRNAs ... available for evaluating the accuracy of predicted microRNA:target interactions. Recently, a dataset ... microRNA-associated mRNA transcripts was identified by immuno-precipitation (IP) of the RNA-induced silencing ... reveals enrichment for defining characteristics of functional microRNA target interactions, including structural accessibility of target...
  • miRExpress

  • Referenced in 3 articles [sw29587]
  • analyzing high-throughput sequencing data for profiling microRNA expression. Conclusion: We develop miRExpress, which...
  • miRcode

  • Referenced in 1 article [sw34970]
  • miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Summary ... Although small non-coding RNAs, such as microRNAs, have well-established functions in the cell ... inhibitory decoys or as regulatory targets of microRNAs, but such interactions are still poorly explored ... facilitate the study of microRNA–lncRNA interactions, we implemented miRcode: a comprehensive searchable...
  • multiMiR

  • Referenced in 1 article [sw32133]
  • Bioconductor/R package multiMiR: Integration of multiple microRNA-target databases with their disease and drug associations ... microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA ... miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe...
  • CellMiner

  • Referenced in 1 article [sw17277]
  • transcripts for 22,379 genes and 360 microRNAs along with activity reports ... doxorubicin activity; identification of colon-specific genes, microRNAs, and drugs; microRNAs related...
  • Sylamer

  • Referenced in 2 articles [sw11231]
  • find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data...
  • RBMMMDA

  • Referenced in 2 articles [sw22491]
  • RBMMMDA: predicting multiple types of disease-microRNA associations. Webserver of RBMMMDA: In addition, we built...