Pinned Repositories
avTAD
Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).
ChromatinCompartments
Compartments calling for published Hi-C datasets
DPDchrom_input_parser
fontanka
Fontanka is a set of tools to work with fountains in Hi-C data. It aims to provide a flexible Python API and specialized CLI for calling fountains from cool Hi-C files.
pairtools
CLI tools to process mapped Hi-C data
RedClib
Red-C data processing
rklib
Rabin-Karp implementation of sequence substring search for DNA/RNA
GEOparse
Python library to access Gene Expression Omnibus Database (GEO)
cooltools
The tools for your .cool's
pairtools
Extract 3D contacts (.pairs) from sequencing alignments
agalitsyna's Repositories
agalitsyna/RedClib
Red-C data processing
agalitsyna/avTAD
Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).
agalitsyna/fontanka
Fontanka is a set of tools to work with fountains in Hi-C data. It aims to provide a flexible Python API and specialized CLI for calling fountains from cool Hi-C files.
agalitsyna/ChromatinCompartments
Compartments calling for published Hi-C datasets
agalitsyna/DPDchrom_input_parser
agalitsyna/pairtools
CLI tools to process mapped Hi-C data
agalitsyna/rklib
Rabin-Karp implementation of sequence substring search for DNA/RNA
agalitsyna/Teaching_materials
agalitsyna/WinterSchool
agalitsyna/bioconda-recipes
Conda recipes for the bioconda channel.
agalitsyna/bioframe
Pandas utilities for tab-delimited and other genomic data files
agalitsyna/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
agalitsyna/cooltools
The tools for your .cool's
agalitsyna/distiller-nf
A modular Hi-C mapping pipeline
agalitsyna/GEOparse
Python library to access Gene Expression Omnibus Database (GEO)
agalitsyna/Gyrase_Topo-seq
Exploring gyrase cleavage sites accross E. coli W3110 genome
agalitsyna/hg
a python api for higlass
agalitsyna/hicrep
Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
agalitsyna/inspectro
Hi-C spectral analysis workflow
agalitsyna/MotifsSearch
In-lab cases of motifs search and manipulations
agalitsyna/MS-AdvancedBioLab-Skoltech
Lipidomics mass-spectrometry analysis for hometask and course project at AdvancedBioLab course at Skoltech
agalitsyna/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
agalitsyna/open2c_examples
agalitsyna/polychrom_workbench
agalitsyna/pySTATIS
Python implementation of STATIS for analysis of several data tables
agalitsyna/resgen-python
agalitsyna/rnadnatools
Tools for RNA-DNA data anipulation
agalitsyna/sc_dros
agalitsyna/TADcalling
agalitsyna/Teaching_materials_Skoltech-Bioinformatics-2020
"Multiple Global Alignment. Multiple Local Alignment" seminar at Skoltech "Bioinformatics" course by Mikhail Gelfand