• Bismark

• Referenced in 5 articles [sw23504]
• data which performs both read mapping and methylation calling in a single convenient step ... context and enables bench scientists to visualize and interpret their methylation data soon after...

• CodonO

• Referenced in 2 articles [sw17252]
• minimization, mRNA stability, codon context, tRNA richness, CpG suppression, DNA methylation, and tissue or organ...

• Repitools

• Referenced in 1 article [sw20385]
• gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation...

• Bisulfighter

• Referenced in 3 articles [sw23508]
• sample, and to detect differentially methylated regions (DMRs) between paired samples. Although numerous tools have ... evaluated on simulated data with various mC contexts, read qualities, sequencing depths and DMR lengths...

• ParticleMDI

• Referenced in 1 article [sw35255]
• approach for performing cluster analysis in a context where observational units have data arising from ... gene expression, copy number variation, DNA methylation, protein expression and microRNA data. We identify...

• Mathematica

• Referenced in 6343 articles [sw00554]
• Almost any workflow involves computing results, and that...

• Matlab

• Referenced in 13488 articles [sw00558]
• MATLAB® is a high-level language and interactive...

• R

• Referenced in 9832 articles [sw00771]
• R is a language and environment for statistical...

• Bioconductor

• Referenced in 320 articles [sw04205]
• Bioconductor provides tools for the analysis and comprehension...

• LIBSVM

• Referenced in 1185 articles [sw04879]
• LIBSVM is a library for Support Vector Machines...

• ElemStatLearn

• Referenced in 1478 articles [sw11049]
• R package ElemStatLearn: Data sets, functions and examples...

• GATK

• Referenced in 17 articles [sw12019]
• The genome analysis toolkit: a MapReduce framework for...

• C4.5

• Referenced in 1162 articles [sw12176]
• C4.5: programs for machine learning. (C4.5 has been...

• KEGG

• Referenced in 275 articles [sw13866]
• KEGG: Kyoto Encyclopedia of Genes and Genomes. KEGG...

• Samtools

• Referenced in 22 articles [sw14583]
• Samtools is a suite of programs for interacting...

• Keras

• Referenced in 183 articles [sw15491]
• Keras: Deep Learning library for Theano and TensorFlow...

• FastQC

• Referenced in 8 articles [sw16946]
• FastQC: A quality control tool for high throughput...

• FASTX

• Referenced in 2 articles [sw17090]
• The FASTX-Toolkit is a collection of command...

• Trimmomatic

• Referenced in 6 articles [sw17091]
• Trimmomatic: a flexible trimmer for Illumina sequence data...

• DAVID

• Referenced in 63 articles [sw17292]
• The DAVID Gene Functional Classification Tool: a novel...