DeepMP is a convolutional neural network (CNN)-based model that takes information from Nanopore signals and basecalling errors to detect whether a read is methylated or not.
CoSBI (Coherent and Shifted Bicluster Identification) is a scalable subspace clustering algorithm to identify the complete set of combinatorial chromatin modification patterns across the entire genome.
histoneHMM is a software to analyse ChIP-seq data of histone modifications with broad genomic footprints like H3K27me3. It allows for calling modified regions in single samples as well as for calling differentially modified regions in a comparison of two samples.
miRMOD is the first windows based standalone GUI tool to identify and analyze non templated nucleotide additions and trimming at both the termini of the miRNA sequences in NGS data.
HMCan is Hidden Markov Model based tool that is developed to detect histone modification in cancer ChIP-seq data. It applies three correction steps to the data: copy number correction, GC bias correction and noise level correction.
HMCan-diff is a method designed specially to detect changes of histone modifications in ChIP-seq cancer samples or between a cancer sample and a normal control. HMCan-diff explicitly corrects for copy number bias as well as for other ChIP-seq technical biases such as GC-content and mappability biases, and variable levels of signal-to-noise in different samples. HMCan-diff uses a three state hidden Markov model to detect regions of differential histone modifications.
iRNA-PseColl is seamless platform for identifying the occurrence sites of different RNA modifications by incorporating collective effects of nucleotides into PseKNC
iRNA-3typeA web-server allows for simultaneously identifying the most frequently observed N1-methyladenosine (m1A), N6-methyladenosine (m6A) and adenosine to inosine (A-to-I) modifications in both H. sapiens and M. musculus transcriptomes.
The tRNAmod is a web-server for the prediction of transfer RNA (tRNA) modifications. Post-transcriptional modifications of tRNA plays a major role in their functionality. It provides both flexibility as well as rigidity and fine tune tRNA structure for the maximum performance.
