Omics · study · 2026
Ryder: Epigenome Normalization and Variable Feature Identification
Listed in NCBI GEO
Sequencing-based epigenomic profiling significantly advances our understanding of chromatin regulation, yet inherent technical variability complicates accurate cross-sample comparisons.
Description
We introduce Ryder, a flexible Python package leveraging stable internal reference regions to perform robust genome-wide normalization. Ryder effectively reduces technical artifacts, distinguishes biological signals, and identifies variable genomic regions across diverse assays, including DNase-seq, ATAC-seq, MNase-seq, and ChIP-seq, with or without spike-in controls.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE300nnn/GSE300647 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE300647 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1281605 ncbi.nlm.nih.gov/bioproject/PRJNA1281605 ↗
project · from NCBI GEO
- PubMed 41889905 pubmed.ncbi.nlm.nih.gov/41889905 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Genome binding/occupancy profiling by high throughput sequencing · Homo sapiens · Mus musculus
- From keywords
- Life Sciences
Provenance · 1 source records, 8 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE300647 | 15 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:genome-binding-occupancy-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[organism].NCBITaxon:10090 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| concepts[organism].NCBITaxon:9606 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |