autosome.org

We present a convolutional network for predicting gene expression and sequence variant effects using data obtained by massive parallel reporter assays, winner of the DREAM2022 promoter challenge. Check the main repo (yeast) and the recent application to the human MPRA data.

The identification of allele-specific events from allelic read counts is non-trivial due to multiple sources of technical and biological variability, which induce data-dependent biases and overdispersion. We designed MIXALIME, a computational framework for calling allele-specific events in diverse omics data with a repertoire of statistical models accounting for read mapping bias and copy-number variation, read more.

This webserver annotates a given list of SNPs with allele-specific binding events across a wide range of transcription factors and cell types using ADASTRA that is constructed through the meta-analysis of more than 15000 ChIP-Seq experiments, read more.

ChIPMunk is a fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping. Now classic and dinucleotide versions come in a single updated package, read more.

MAtrix CompaRisOn and PrEdicting Regulatory Functional Effect by Approximate P-value Estimation toolbox allows estimating motif P-values, comparing PWMs using natural Jaccard similarity measure and motif-based analysis of regulatory SNVs for mono- and dinucleotide PWMs, read more here and there.

Transcription Factor Motif Location Toolbox is an interactive web application to scan DNA sequences for transcription factor binding sites (TFBS) with position weight matrices presented in HOCOMOCO model collection, see in action.

Papolarity is a Python package for analysis of positional biases in transcript-level short read coverage profiles obtained by ribosome profiling (Ribo-Seq) or other transcriptomic -Seq data, read more.

Pasio is a software tool to simplify and denoise short read coverage profiles arising from high-throughput sequencing data such as ChIP-Seq, DNase-Seq, ATAC-Seq and other -Seq experiments, read more.

Straightforward yet Powerful Rapid SuperAlphabet Representation Utilized for motif Search is as practical command-line ChIPMunk companion
intended for motif finding with mono- and dinucleotide position weight matrices, read more.

A simple bioinformatics tool for visualization of genomic signal tracks in user-defined genomic windows, either arbitrary selected by genomic coordinates or anchored to particular transcripts or genes, read more.