Here I listed the technical development side of my PhD work, which is to create an integrated pipeline for low input epigenome profiling for biologist. This pipeline contains two parts: one is wet lab protocol package SmallCell, which enables researchers to profiling transcriptome and epigenome from ~1000~2000 cells; the other part is the dry lab code package InterSeq, which enables intersect different types of sequencing data based on their distribution pattern.
A wet lab bench protocol package for profiling transcriptome and epignenome from low input materials.
To see a detailed description, go to https://github.com/sheng-liu/SmallCell/blob/master/SmallCell.md
SmallCell-suit
is a wet lab bench protocol package for profiling transcriptome and epigenomic
information, namely histone modification and DNA methylation, from 1000~2000
cells. It is designed for surveying epigenetic information of rare cell
populations in vivo at locus-specific and genome-wide scales.
Individual
protocol can be accessed from:
o Low input chromatin
immunoprecipitation (ChIP) with smallcellChIP
https://github.com/sheng-liu/smallcellChIP.git
o Low input RNA isolation and
reverse transcription with smallcellRNA
https://github.com/sheng-liu/smallcellRNA.git
o Low input bisulfite
conversion and Sanger Sequencing with smallcellDNAme
https://github.com/sheng-liu/smallcellDNAme.git
A
bioinformatic tool for intersecting multiple types of epigenomic datasets.
To see a
detailed description, go to https://github.com/sheng-liu/InterSeq/blob/wiki/ProjectHome.md
Individual package can be accessed from:
o Calculations from a bam file
with SeqData
https://github.com/sheng-liu/SeqData.git
o Interface tables to flowCore with SeqFrame
https://github.com/sheng-liu/SeqFrame.git
o Graphical interface for
visualization and gating with SeqViz
https://github.com/sheng-liu/SeqViz.git
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Package names |
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SmallCell |
smallcellChIP smallcellRNA smallcellDNAme |
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InterSeq |
SeqData SeqFrame SeqViz |
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