This ChIP-Seq pipeline is based off the ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline specifications (by Anshul Kundaje) in this google doc. IMPORTANT: Read Caper's README ...

To run MACS in a 64-bit environment, Python for the 64-bit CPU should be installed. Data: We selected several ChIP-seq and control data sets from ENCODE 20 and made them accessible at http ...

Before you start peak calling, you need to check the quality of your ChIP-seq data. This includes assessing ... You can also use tools like ENCODE or ChIPQC to compare and optimize your peak ...

The ideal biclusters should contain similar values with very low variance. We applied our algorithm on ChIP-seq datasets recently released from the ENCODE project and uncovered meaningful biclusters ...

Background IKZF1 (Ikaros), IKZF2 (Helios) and IKZF3 (Aiolos) are candidate genes for Systemic Lupus Erythematosus (Pmeta<5x10–8). The proteins are members of the Kruppel zinc finger family of ...

You need to reinstall pipeline's Conda environment. It's recommended to do this for every version update. (Optional for Conda) DO NOT USE A SHARED CONDA. INSTALL YOUR ...