The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
Open accessAbstract
Summary: Due to the rapidly increasing scale and diversity of epigenomic data, modular and scalable analysis workflows are of wide interest. Here we present snakePipes, a workflow package for processing and downstream analysis of data from common epigenomic assays: ChIP-seq, RNA-seq, Bisulfite-seq, ATAC-seq, Hi-C and single-cell RNA-seq. snakePipes enables users to assemble variants of each workflow and to easily install and upgrade the underlying tools, via its simple command-line wrappers and yaml files. Availability and implementation: snakePipes can be installed via conda: `conda install -c mpi-ie -c bioconda -c conda-forge snakePipes’. Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online. Supplementary information: Supplementary data are available at Bioinformatics online.
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Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219
Salmon provides fast and bias-aware quantification of transcript expression
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017) · Nature Methods · doi:10.1038/nmeth.4197 · Cited by 12,700
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368
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Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017) · Nature Biotechnology · doi:10.1038/nbt.3820 · Cited by 4,001
Function and information content of DNA methylation
Schübeler, D. (2015) · Nature · doi:10.1038/nature14192 · Cited by 2,060
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Imakaev, M., Fudenberg, G., McCord, R. P., Naumova, N., Goloborodko, A., Lajoie, B. R., Dekker, J., & Mirny, L. A. (2012) · Nature Methods · doi:10.1038/nmeth.2148 · Cited by 1,423
SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes
Krueger, F., & Andrews, S. R. (2016) · F1000Research · doi:10.12688/f1000research.9037.2 · Cited by 163
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Fernández, J. M., de la Torre, V., Richardson, D., Royo, R., Puiggròs, M., Moncunill, V., Fragkogianni, S., Clarke, L., Flicek, P., Rico, D., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.10.021 · Cited by 151
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Metadata
- Authors
- Bhardwaj, V., Heyne, S., Sikora, K., Rabbani, L., Rauer, M., Kilpert, F., Richter, A. S., Ryan, D. P., & Manke, T.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-05-27
- Volume
- 35
- Issue
- 22
- Pages
- 4757-4759
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2947747649
- Cited by
- 196
- References
- 11
- FWCI
- 26.54
- Type
- journal article
- Language
- en
- Open access
- hybrid
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