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SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of differ…
Opensource Python project for cancer radiation treatment planning [AAPM'23]
Modeling of time series data for CRISPR KO experiments
Fast and accurate in silico inference of HLA genotypes from RNA-seq
AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current …
Cell line HLA types and neoepitope catalog from TCLP
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
Install GISTIC2 by one line code; GISTIC2 docker image
A cross-platform proteomics data analysis suite
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
IGM with new assignment step for HiC, requires linear scaling only
trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.
Code for the ProteinMPNN paper