seqcode
Collection of projects related to DNA sequencing data processing & regulatory genomics analyses
Penn State University, University Park, PA
Pinned Repositories
allo
Allo: a multi-mapped read rescue strategy for gene regulatory analyses
Bichrom
Interpretable bimodal network for transcription factors binding site prediction
chexmix
ChExMix: the ChIP-exo mixture model
chromosom
ChromoSOM: a Self-Organizing Map for analyzing chromatin interactions
cross-species-domain-adaptation
Codebase for the domain adaptation (cross-species TF binding prediction) project.
IDEAS
Jointly characterizing epigenetic dynamics across multiple cell types
miniMDS
seqcode-core
SeqCode: Java code for the analysis of high-throughput sequencing data
sequnwinder
SeqUnwinder: a platform for deconvolving motifs associated with genomic labels
stamp
STAMP
seqcode's Repositories
seqcode/IDEAS
Jointly characterizing epigenetic dynamics across multiple cell types
seqcode/Aydin_2019_iAscl1-vs-iNeurog2
Contains analysis scripts used to process data for Aydin, et al. 2019 manuscript
seqcode/encodedream
Code for our contribution to the ENCODE/DREAM challenge
seqcode/pyseqcode
pyseqcode: Python code for the analysis of high-throughput sequencing data
seqcode/encode_imputation_submission
Directory for encode imputation model submission.
seqcode/heatmap
creates heatmap from BAM
seqcode/IDEAS-trackhubs
UCSC Genome Browser trackhub definition files for IDEAS segmentation results
seqcode/mahonylab-ucsc-trackhubs
Trackhubs for collaborative projects
seqcode/matplotlib-examples
Prettier figures in matplotlib
seqcode/vinayachandran_2017_figs
Scripts to re-create figures from Vinayachandran, et al. Genome Research 2018