Articles

SCI

DA Datirium

Multi-factor Differential Accessibility/Binding Analysis with DiffBind: Understanding Complex…

You’ve performed multiple ChIP-Seq, ATAC-Seq, or CUT&RUN experiments across different conditions, time points, or treatments. Now you want…

Apr 01, 2026 · 7 min read · 0 claps #diffbind #chip-seq #atac-seq

BIO GEN MDA SCI TCH

DA Datirium

Multi-factor analyses in SciDAP: design formulas and other settings

For differential expression analysis of bulk RNA-Seq data, SciDAP provides pairwise DESeq2 pipeline and multifactor DESeq2 LRT/Wald Step…

Jan 20, 2026 · 9 min read · 0 claps #rna-seq #chip-seq #experimental-design

BIO GEN MDA SCI TCH

DA Datirium

Differential gene expression analysis with DESeq2: Making Sense of RNA-Seq Counts

When biologists run an RNA-seq experiment, the raw output is essentially a giant spreadsheet of numbers: how many sequencing reads came…

Jan 14, 2026 · 5 min read · 0 claps #rna-seq #rna-sequencing #bioinformatics

GEN AI BIO

DA Datirium

New SciDAP Workflow: WGS Metagenomics — Taxonomic Classification and Functional Analysis

How to: User-friendly metagenomic shotgun sequencing analysis in SciDAP

Jan 14, 2025 · 5 min read · 1 claps #metagenomics #shotgun #microbiome

BIO GEN AI

DA Datirium

CUT&RUN and CUT&Tag data analysis in SciDAP

CUT&RUN and CUT&Tag are methods used to identify the DNA sequence where DNA binding proteins bind DNA in chromatin. Developed in the…

Jul 02, 2024 · 4 min read · 0 claps #cut-and-tag #cut-and-run #epigenomics

GEN

DA Datirium

Live on BioRxiv: Methods Paper on scMultiome Multiome Data Analysis in SciDAP

How to guide for 10x scMultiome, scRNA-seq and scATAC-seq data analysis in SciDAP: Cell Ranger, Seaurat, Harmony, doublet finder and…

Mar 10, 2024 · 1 min read · 0 claps #scrna-seq #scmultiome #scatac-seq

DA Datirium

HOMER Motif Enrichment Analysis in SciDAP

Motif analysis is used to identify short sequences (motifs) that are over-represented in target sequences compared to background. These can…

Feb 21, 2024 · 7 min read · 0 claps #motif-analysis #transcription-factor #homer

GEN AI BIO

DA Datirium

New SciDAP Workflow: 16S Metagenomic analysis with QIIME2

How to run Qiime2 microbiome analysis in SciDAP: QC, Alpha rarefaction plots, taxonomic classification, differential analysis, PCOA

Sep 27, 2023 · 7 min read · 1 claps #microbiome #qiime2 #metagenomics

GEN

DA Datirium

New SciDAP Workflow: Germline Variant Calling pipeline with GATK4

How to do variant calling from Whole Genome Sequencing and Exome Sequencing data in SciDAP

Jul 26, 2023 · 5 min read · 0 claps #gw #exome-sequencing #variant-calling

BIO GEN

DA Datirium

The single cell mess at NCBI: how GEO/SRA store 10x Genomics scRNA-seq data and how to load them…

10x Genomics single cell workflow

May 26, 2023 · 6 min read · 1 claps #bioinformatics-analysis #ncbi-geo-sra #srr-accession-number

BIO SCI GEN MKT MDA TCH

DA Datirium

New SciDAP workflow: miRNA-seq analysis

Micro RNA (miRNA) are small RNA molecules that play an important role in regulating gene expression. Data from sequencing experiments…

Apr 26, 2023 · 4 min read · 0 claps #mirna #mirna-sequencing #scidap

ART BIO TCH GEN

DA Datirium

SciBox: Optimized Hardware for Faster NGS Data Analysis in SciDAP

In an earlier blog post, we talked about SciDAP architecture for processing NGS data. To enhance security and privacy of users’ data, we…

Dec 16, 2022 · 2 min read · 1 claps #ngs-data-analysis #scidap #bioinformatics

BIO ECO GEN

DA Datirium

SciDAP Supports Multi-omics Study Linking Vitamin D Deficiency to Allergies

Vitamin D (VD) is considered an essential factor, that tempers damaging and boosts healthy immune responses. Its deficiency has been linked…

Nov 21, 2022 · 3 min read · 1 claps #rna-seq #scidap #allergy-treatment

BIO

DA Datirium

Merging FASTQs: What to do if you have several FASTQ files for each sample?

How to merge fastq files

Sep 26, 2022 · 4 min read · 3 claps #fastq #chip-seq #bioinformatics

BIO GEN

DA Datirium

The Easiest Way for Biologists to Explore Their NGS Data

Next generation sequencing (NGS) generates so much data that analysis is struggling to keep up. Analysis relies on trained data scientists…

Aug 25, 2022 · 3 min read · 0 claps #rna-seq #atac-seq #scrna-seq

MDA SPT SCI

DA Datirium

Paper Highlight: SciDAP Used in a Recent Study of B Cell Acute Leukemia published in Nature…

Nayak, R.C., Chang, K.H., Singh, A.K. et al. Nuclear Vav3 is required for polycomb repression complex-1 activity in B-cell lymphoblastic…

Jul 22, 2022 · 2 min read · 0 claps #datirium #scidap #deeptools

GEN

DA Datirium

New collection of reproducible CWL pipelines for single cell multiome data analysis

Michael Kotliar, a bioinformatician , will present a new collection of CWL pipelines for analysis of single-cell data…

Jul 13, 2022 · 1 min read · 0 claps #scidap #single-cell-analysis #common-workflow-language

SCI

DA Datirium

Datirium Receives Phase II TVSF Award from the State of Ohio to Develop its Scientific Data…

May 10, 2022

Jul 05, 2022 · 2 min read · 0 claps #datirium #scidap #financing