small RNAs & RBPs

MIRZA-G

MIRZA-G is a tool and a model used for miRNA target prediction.

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snoRNA human atlas

Catalog of snoRNA loci in the human genome.


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snoRNA Hybrid Search Pipeline

A pipeline to discover snoRNA-target chimeric reads in CLIP/HTS experiments.

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snoRNA chimeras DB

Predictions alignments of putative chimeric reads to putative target sites and snoRNAs.


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PheLiM

Estimation of gene contributions to the phenotype from genome-wide RNA interfence experiment.

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MirZ (discontinued)

MirZ: an integrated microRNA expression atlas and target prediction resource.


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ElMMo3 (discontinued)

ElMMo Target Predictions.

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CLIPZ (discontinued)

Analysis of small RNAseq data.

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Splicing & Polyadenylation

Transcript isoform benchmarking

Online service for evaluating transcript isoform quantification methods.




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Poly(A) site

Repository for 3' end sequencing data. Resource that supports investigations into the polyadenylation programs that operate during changes in cell physiology, during development, and in malignancies.

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TECtool

TECtool is a method that uses mRNA and 3’ end sequencing data to identify novel terminal exons, infer novel transcripts, and annotate CDS for novel transcripts.


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PAQR

PAQR is a method for the polyadenylation site usage quantification from RNA sequencing data and infers drops in the read coverage profile of RNA-seq libraries at positions of annotated poly(A) sites. In this way, the relative poly(A) site usage can be calculated for genes whose 3' UTR length can vary depending on the chosen cleavage site.

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KAPAC

KAPAC stands for k-mer activity on polyadenylation site cchoice and is the method that infers position-dependent activities of sequence motifs on 3' end processing from changes in poly(A) site usage between conditions.



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