Juicer / Juicebox
Hi-C processing and visualization from the Aiden lab ecosystem.
Open resourceCurated list
Hi-C and 3D Genome Analysis
HiC-Pro
Flexible Hi-C processing for a wide range of library types.
Open resourceCooler / Cooltools
Python ecosystem for contact matrices, insulation, saddle plots, and related analyses.
Open resourceFAN-C
Comprehensive Hi-C analysis with a Python API.
Open resourceFitHiChIP
HiChIP and PLAC-seq interaction analysis.
Open resourceCurated list
ChIP-seq, CUT&RUN, and CUT&TAG
MACS3
Peak calling for transcription factor and histone modification datasets.
Open resourcedeepTools
BAM and bigWig processing, heatmaps, and profile plots.
Open resourceHOMER
Motif discovery, peak annotation, and ChIP-seq analysis utilities.
Open resourceBowtie 2
Short-read alignment commonly used in chromatin profiling workflows.
Open resourceChIPseeker
R/Bioconductor package for peak annotation and visualization.
Open resourceCurated list
RNA-seq and Nascent Transcription
STAR
Splice-aware RNA-seq aligner often used for nuclear RNA work.
Open resourceHISAT2
Fast spliced aligner with modest memory requirements.
Open resourcefeatureCounts
Gene-level read quantification from aligned reads.
Open resourceDESeq2
Differential expression modeling for count data.
Open resourceedgeR
Differential expression analysis for replicated count experiments.
Open resourceCurated list
ATAC-seq
ENCODE ATAC-seq pipeline
Standardized processing and quality-control workflow.
Open resourceATACseqQC
ATAC-seq quality-control metrics and visualization in R.
Open resourcechromVAR
Transcription factor accessibility variation across samples.
Open resourceCurated list
Image Analysis
Fiji / ImageJ
Extensible image-analysis platform with broad microscopy plugin support.
Open resourceCellProfiler
High-content image-analysis pipelines for nuclear morphology and phenotyping.
Open resourceTrackMate
Fiji plugin for particle and object tracking.
Open resourceNucleusJ
Nuclear morphology and chromatin organization analysis in Fiji.
Open resourceStarDist
Deep-learning nuclear segmentation for microscopy images.
Open resourceCellpose
Generalist cellular and nuclear segmentation models.
Open resourceSite operator software
Microscopy and rendering examples from Gnometrix Labs
CellNucleus.com is operated by Gnometrix Labs. The product pages show software examples and describe current development scope and availability; these links are separate from the curated third-party resources above.