Analyses: We provide a variety of standard and custom sequencing data analyses

   
Transcriptomics RNA-Seq, UMI-based RNA-Seq, High Throughput RNA-Seq (”Drug-Seq”), smallRNA-Seq (miRNA-Seq)
Single-cell analytics Gene expression, Immune profiling (VDJ, VDJ+Gene expression), Epigenome profiling (ATAC, Multiome ATAC + Gene expression)
Spatial genomics GeoMx Digital Spatial Profiling (nanoString)
Visium Spatial transcriptomics (10x Genomics)
Genomics SNP-based demultiplexing of multiplexed data
Exome, Whole Genome sequencing data analyses, SNPs, indels, CNVs
Epigenomics ChIP-Seq/eCLIP-Seq/CUT&RUN/RIP-Seq, ATAC-Seq
Metagenomics 16S rRNA-Seq
Custom analyses Sequencing data analyses for specific lab projects that use standard tools, software packages and/or custom code/script developed by CCBB.
Public Datasets Analyses on public dataset available at NCBI’s GEO database repository
Functional Analyses Advaita’s iPathwayGuide for a full comprehensive functional analysis including pathways/GO terms/mRNAs/upstream regulators/diseases ADVAITA service request
Gene Set Enrichment Analysis (GSEA)
Consultations We provide consultations on experimental design, overview of analyses and costs involved. We can take on both short-term (typically less than a month and about 10 hours of CCBB effort) and long-term collaborative projects involving bioinformatic support.
GEO/SRA uploads We can submit your sequencing data, related sample metadata and the results of analyses to NCBI repositories like Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) for a small service fee.
Flow Cytometry Analysis Custom Flow Cytometry Analysis Pipeline for QC, Visualization, and dimension reduction analysis