SIJAE-WOO

openASO

openASO is a project designed to identify regulatory regions of an RNA that can be targeted by antisense oligonucleotides.

popEVE

meditron

Meditron is a suite of open-source medical Large Language Models (LLMs).

SVAFotate

Alleloscope

Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separately or in combination). Allele-specific estimation allows for the more accurate delineation of copy number states and the detection of subclonal copy-neutral loss-of-heterozygosity and mirrored CNA events. On scATAC-seq data, Alleloscope allows integrative multi-omic analysis of allele-specific copy number and chromatin accessibility for the same cell.

counTR

counTR is a method to detect differential tandem repeat content between different groups of sequencing data

slow5curl

A library and tool for accessing remote BLOW5 files.

igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

decipher

A single-cell analysis toolkit to jointly analyze samples from distinct conditions

hyena-dna

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

m6ABasecaller

An m6A-aware basecalling model to detect m6A modifications at single nucleotide resolution in individual reads (Cruciani, Delgado-Tejedor, Pryszcz et al., BioRxiv 2023)

borzoi

RNA-seq prediction with deep convolutional neural networks.

SuPreMo

Pipeline for generating reference and perturbed sequences for input into predictive models.

gpn

Genomic Pre-trained Network

UTR-LM

deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.

ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

chromoscope

Interactive multiscale visualization for structural variation in human genomes

Iliad

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

HiPhase

Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads

ggthemes

Additional themes, scales, and geoms for ggplot2

oor_design_reproducibility

HiFi-human-WGS-WDL

SHEPHERD

SHEPHERD: Few shot learning for phenotype-driven diagnosis of patients with rare genetic diseases

TxGNN

TxGNN: Zero-shot prediction of therapeutic use with geometric deep learning and clinician centered design

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

BLEEP

Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning

wgs_fusion_pipeline

ipyMolecularNodes

molecular plots in Jupyter, powererd by Blender Geometry Nodes

PyMOL-Wasm

PyMOL-wasm port's binary and html/javascript code