autosome-ru

LegNet

accurate prediction of promoter activity and variant effects from massive parallel reporter assays

vigg_ribonanza

Source code of the Stanford Ribonanza RNA Folding first place solution

MixALime

human_legnet

ADASTRA-pipeline

BABACHI

motif_benchmarks

Benchmarks collection for GRECO TFBS Benchmarking Initiative

ArmNet

macro-perfectos-ape

MACRO-APE and PERFECTOS-APE tools

sarus

SPRY-SARUS motif scanner

ibis-challenge

Repository with source code and metadata for IBIS challenge

papolarity

Tools to deal with coverage profile on a transcript level. Allows to analyse ribosome positional preferences (such as polarity score) based on Ribo-Seq data.

pasio

Pasio is a tool for denoising profiles coming from DNA-sequencing data like ATAC-seq, DNA-seq or ChIP-seq.

sequence_logo

SequenceLogo is a tool for drawing sequence logos of motifs

hocomoco_webapp

Web-site for HOCOMOCO collection of transcription factor binding sites motifs.

mixalime_reproduction_material

Reproduction material for numerical tests in a MixALime paper

ASB-backend

ASB-frontend

draw_motif_logo

Python3 scripts to draw motif logo in svg format

epifactors_webapp

Web-site for EpiFactors database of epigenetic factors, corresponding genes and products.

hocomoco_rsnp_benchmarks

hocomoco_v9

Old version of HOCOMOCO TFBS motif database, version 9: https://autosome.ru/HOCOMOCO

HT-SELEX-kmer-filtering

K-mer filtering algorithm for HT-SELEX data processing

kmer-motif-enrichment

MoLoTool

Sequence Motif Location Tool (MoLoTool)

opera_webface

Webface for OperaHouse (included inside)

PBM_preprocessing

PWM-evaluation-using-SNP-SELEX

Supplementary data for "Positional weight matrices have sufficient prediction power for analysis of noncoding variants"

UDACHA_pipeline

visualize-hoco