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scHiCExplorer. The scHiCExplorer is a software to demultiplex, process, correct, normalize, manipulate, analyse and visualize single-cell Hi-C data. scHiCExplorer supports the mcool file format and stores per cell one Hi-C interaction matrix in it.
Jul 7, 2021 · The embedding into the cooler API guarantees a fast and reliable access to the individual single-cell matrices and facilitates the use of parallel computing to improve analysis performance. The scool format is ideal for single-cell Hi-C data analysis software and is supported by scHiCExplorer (Wolff et al., 2020).
- Joachim Wolff, Nezar Abdennur, Rolf Backofen, Björn A. Grüning
- 10.1093/bioinformatics/btaa924
- 2020
- 2021/07/07
- Introduction
- Related Works
- Galaxy HiCExplorer
- Implementation
- Using HiCExplorer
- Training
- Discussion
- Acknowledgements
- Funding
Chromosome conformation capture (3C) (1) and its successors 4C (2,3), 5C (4) and Hi-C (5) have developed into the standard technologies used in studying the 3D conformation of chromatin. They can provide insights into the processes involved in chromatin folding and gene regulation. Hi-C technology is a well established method to study genome wide i...
Galaxy HiCExplorer is designed as an easy-to-use online service which is accessible through a web browser. Thus, no installation is required. By embedding it into Galaxy (17) and the https://usegalaxy.eu environment, it facilitates reproducible, shareable research as well as easily accessible data analysis. With Galaxy HiCExplorer, researchers can ...
Galaxy HiCExplorer offers a large collection of tools to pre-process, analyse and visualize Hi-C, cHi-C and scHi-C data. In addition to its assay-specific modules, users can benefit from the external pre-processing software for quality control of raw data and mappers such as BWA-MEM or Bowtie2 which are provided on the https://hicexplorer.usegalaxy...
Galaxy HiCExplorer is implemented as a collection of Galaxy tool wrappers and is available on the Galaxy ToolShed. The Galaxy integration is provided for HiCExplorer as well as scHiCExplorer. HiCExplorer and scHiCExplorer are both implemented in Python 3.6 and are available on Bioconda (16). The Knight-Ruiz correction and the MinHash approximate k-...
Installation and usage
Galaxy HiCExplorer can be used as a web server and is accessible via https://hicexplorer.usegalaxy.eu. All presented tools are publicly available and may be used without any required registration. Unregistered users are provided with 11 GB storage space, while registered users are granted 250GB. Registered users have the opportunity to apply for more storage. Users are strongly encouraged to use https://hicexplorer.usegalaxy.euweb server if high compute resources are required. Galaxy HiCExplo...
To support researchers in their analysis of Hi-C, cHi-C or scHi-C data, tutorials and a detailed documentation are available on https://hicexplorer.readthedocs.io and https://schicexplorer.readthedocs.io. As presented in (29), the guided tours for novice users of Galaxy as well as the Galaxy HiCExplorer specific tutorial are available on the Galaxy...
The presented web server on https://hicexplorer.usegalaxy.eugives researchers the opportunity to focus on their data analysis in a user friendly, reproducible and computationally powerful environment. With the deep integration of HiCExplorer into the Galaxy environment, users are now able to combine their Hi-C, cHi-C (Promoter cHi-C, HiChIP) or scH...
We thank Simon Bray and Anup Kumar of the Bioinformatics group at the Albert-Ludwigs-Universität of Freiburg im Breisgau, Germany and Simon Rapple for proof reading the manuscript.
German Science Foundation [CRC992 ‘Medical Epigenetics’ to L.R., T.M., R.B., B.G.; GI 747/2-1, GI 747/3-1 to R.G.]; German Federal Ministry of Education and Research [031 A538A de.NBI-RBC awarded to R.B.]; German Federal Ministry of Education and Research [031 L0101C de.NBI-epi awarded to B.G.]; R.B. was supported by the German Research Foundation ...
- Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Back...
- 2020
scHiCExplorer ¶. Set of programs to process, normalize, analyse and visualize single-cell Hi-C data ¶. Citation ¶. Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A Grüning.
Joachim Wolff was born on 22 July 1920 in Stargard, Pomerania, Germany [now Stargard Szczecinski, Zachodniopomorskie, Poland]. He was an actor, known for Trauer muß Elektra tragen (1966), Kümo Henriette (1979) and The Captain from Köpenick (1956). He died on 30 November 2000.
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Jul 9, 2022 · HiCExplorer has the highest intersection of detected loops with chromosight, but chromosight also provides the highest number of detected loops. The intersection of detected loops with cooltools is similar to HiCCUPS; the number of intersecting loops with HOMER, Fit-Hi-C 2, and Peakachu is lower.
Jun 13, 2018 · Training and a documentation are crucial to enable as many scientists as possible to use and understand the Galaxy HiCExplorer. To introduce scientists who are new to Galaxy a guided tour through the Galaxy interface is provided as well as a tour to learn Hi-C data analysis.
