Supplementary files accompanying eLife publication entitled "hiExM: high-throughput expansion microscopy enables scalable super-resolution imaging"

Notes on single-cell Hi-C technologies, tools, and data

Uniform Manifold Approximation and Projection

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

Foreign Contamination Screening caller scripts and documentation

A lightweight Python module to read and write FASTA sequence records

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Hybrid error correction of long reads using colored de Bruijn graphs

Align proteins to genomes with splicing and frameshift

Double_Cut_Join_Dosage_Sensitive

A collection of tools for Hi-C data analysis

🔬 ♌ Bacterial ribosomal RNA predictor

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

scripts to process, join, split, or add new proteins to a supermatrix alignment using hmms

A (very) simple script to QC Hi-C data.

htop - an interactive process viewer

OrthoFiller: Identifying missing annotations for evolutionarily conserved genes.

de Bruijn CompAction in Low Memory

One true awk

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

Single-cell Transcriptome and Regulome Analysis Pipeline

Tools to analyze Dip-C (or other 3C/Hi-C) data

use long sequenced reads to close gaps in assemblies

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Long-reads Gap-free Chromosome-scale Assembler

Fast, flexible and extensible genome browser.

Meta-pipeline to identify transposable element insertions using next generation sequencing data

Extensive de-novo TE Annotator