• Bioconductor

• Referenced in 320 articles [sw04205]
• analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language...

• Cytoscape

• Referenced in 82 articles [sw09080]
• integrating biomolecular interaction networks with high-throughput expression data and other molecular states into...

• DEseq

• Referenced in 59 articles [sw10344]
• mean dependence in count data from high-throughput sequencing assays and test for differential expression...

• RegulonDB

• Referenced in 53 articles [sw25948]
• mapped promoters coming from our own high-throughput mapping efforts. RegulonDB v.6.0 now expands beyond...

• MCODE

• Referenced in 49 articles [sw35748]
• false positives in data from high-throughput interaction techniques. The program is available from...

• ArrayExpress

• Referenced in 42 articles [sw29723]
• Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data...

• FAMT

• Referenced in 32 articles [sw11123]
• multiple testing procedures for high-throughput data as proposed by Friguet...

• Samtools

• Referenced in 22 articles [sw14583]
• suite of programs for interacting with high-throughput sequencing data. It consists of three separate ... HTSlib: A C library for reading/writing high-throughput sequencing data. Samtools and BCFtools both...

• DESeq2

• Referenced in 27 articles [sw41938]
• mean dependence in count data from high-throughput sequencing assays and test for differential expression...

• VAMPnets

• Referenced in 19 articles [sw32927]
• such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transformation...

• iDNA-Methyl

• Referenced in 19 articles [sw22423]
• predictor will become a very useful high-throughput tool for basic research and drug development...

• Prnam-PC

• Referenced in 18 articles [sw22422]
• predictor will become a useful high-throughput tool for identifying methylation sites...

• CellProfiler

• Referenced in 17 articles [sw18751]
• open-source system designed for flexible, high-throughput cell image analysis, CellProfiler. CellProfiler can address...

• iHSP-PseRAAAC

• Referenced in 16 articles [sw25193]
• highly desirable to develop a high-throughput computational tool in this regard. To take...

• STAR

• Referenced in 15 articles [sw02515]
• aligner. Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging...

• DRAGON

• Referenced in 14 articles [sw00220]
• well as for similarity analysis and high-throughput screening of molecule databases. Dragon...

• GOTM

• Referenced in 9 articles [sw13869]
• Gene Ontology hierarchies. Microarray and other high-throughput technologies are producing large sets of interesting ... with other gene sets from other high-throughput analyses. GOTree Machine generates a GOTree...

• HTSeq

• Referenced in 8 articles [sw16898]
• Python framework to work with high-throughput sequencing data. Motivation: A large choice of tools ... standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project...

• RAST

• Referenced in 8 articles [sw17158]
• shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided ... wide range of researchers. Results: A high-throughput pipeline has been constructed to provide high...

• DEGseq

• Referenced in 11 articles [sw07998]
• expressed genes from RNA-seq data. High-throughput RNA sequencing (RNA-seq) is rapidly emerging...