Stars
Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
R package for detecting doublets in single-cell RNA sequencing data
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
[NeurIPS 2024] Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA
Pileup biallelic SNPs from single-cell and bulk RNA-seq data
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Gfapy: a flexible and extensible software library for handling sequence graphs in Python
Tools for manipulating sequence graphs in the GFA and rGFA formats
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
jianhong / hicar
Forked from nf-core/hicarThis pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
ChIP-seq peak caller for reads mapped to a graph-based reference genome
Official PyTorch implementation of Learning to (Learn at Test Time): RNNs with Expressive Hidden States
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Fast alignment and preprocessing of chromatin profiles
sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale