ScEpiSearch

About

Studying single cells using epigenome helps in highlighting active and poised regulatory regions and mechanisms in cells. With rise in number of single cell epigenome profiles from several organisations, there is potential to use it for many biomedical applications. Hence, ScEpiSearch aims to provide a platform to facilitate a primary step in single cell epigenome analysis. ScEpiSearch allows to search matching cells using single-cell epigenome profile. In current version user can submit single cell open chromatin signal to search existing single-cell RNAseq and single-cell ATACseq profiles and perform some task of analysis.

Note : Cross-batch and Cross-species embedding is available in stand-alone version.

Mirror Link
http://reggen.iiitd.edu.in:1207/episearch/

Standalone Version Download

One can use standalone system for querying large cells and Data Privacy concerns. Cross-batch and Cross-species embedding is available in stand-alone version.

Requirement File

dependency Installation Readme File

Download Tool

Statistics

Reference Dataset	Sample Size
Single Cell Expression (Human)	2,239,727
Single Cell Epigenome (Human)	742297
Single Cell Expression (Mouse)	2141797
Single Cell Epigenome (Mouse)	81173

SOME SAMPLE QUERY RESULTS :

Query Type	URL
Myoblast(Human)	http://reggen.iiitd.edu.in:1207/episearch/?job=-ggbqir0do-hlpsn5gn7
Neuron (Mouse)	http://reggen.iiitd.edu.in:1207/episearch/?job=-puamhnftl-zkm98ya79
GM (Cross Species)	http://reggen.iiitd.edu.in:1207/episearch/?job=-uhibbslst-d5c8lzijd

Search Form

Count file should be "," separated.
Peak file should be "tab" separated.

Select Reference Database:
HUMAN (hg19) MOUSE (mm9)
CROSS-SPECIES (HUMAN (hg19) -> MOUSE)
Select Active/Poised state:
Active Genes (Top 1000 Genes)
Active + Poised Genes (Top 2000 Genes)
Select Ref Data Annotation Type :
Annotated Cells Both Annotated & Unannotated Cells

Email ID: Optional

No. of Results Per Study : Required

No. of Top clusters to match : Required

Upload Epigenome Count File : Required

Accepted file extension: .txt.zip, .txt.gz (without headers)

Upload Epigenome Peak Location File : Required

Accepted file extension: .bed.zip, .bed.gz (without headers)

ACCURATE FASTER

NOTE : User will immediately get a result URL, so email is not necessary. However as ACCURATE search takes time, user can get job completion notification, if email is provided.