• HTqPCR

• Referenced in 2 articles [sw29359]
• HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R. Motivation ... solutions are not amenable to the tandem analysis of multiple assays. This is problematic when ... analyzed in a high-throughput facility. Results: We have developed HTqPCR, a package ... computing environment, to enable the processing and analysis of qPCR data across multiple conditions...

• DESeq2

• Referenced in 27 articles [sw41938]
• R/Bioconductor package DESeq2: Differential gene expression analysis based on the negative binomial distribution. Estimate variance ... mean dependence in count data from high-throughput sequencing assays and test for differential expression...

• CONFAC

• Referenced in 4 articles [sw35535]
• CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets. The advent ... comparative genomics with high-throughput gene expression analysis. Here we describe the conserved transcription factor ... site (CONFAC) software that enables the high-throughput identification of conserved transcription factor binding sites ... genes using a Mann–Whitney U-test. Analysis of random gene sets demonstrated that using...

• MEGAN

• Referenced in 17 articles [sw33189]
• known sequences. Most published studies use the analysis of paired-end reads, complete sequences ... sequencing-by-synthesis technologies with very high throughput are paving the way to low-cost ... computer program that allows laptop analysis of large metagenomic data sets. In a preprocessing step...

• Snakemake

• Referenced in 4 articles [sw23580]
• especially useful for building high-throughput sequencing data analysis pipelines and present examples from this...

• GOTM

• Referenced in 9 articles [sw13869]
• Gene Ontology hierarchies. Microarray and other high-throughput technologies are producing large sets of interesting ... created a web-based tool for data analysis and data visualization for sets of genes ... analysis but is adaptable for use with other gene sets from other high-throughput analyses ... user friendly data navigation and visualization. Statistical analysis helps users to identify the most important...

• EGAD

• Referenced in 1 article [sw39967]
• times. To permit high-throughput analysis of gene networks, we have implemented...

• ACUA

• Referenced in 2 articles [sw27733]
• codon usage analysis. Currently available codon usage analysis tools lack intuitive graphical user interface ... been developed to perform high throughput sequence analysis aiding statistical profiling of codon usage...

• DropPy

• Referenced in 1 article [sw38551]
• High-throughput analysis of contact angle goniometry data using DropPy. At present, surface wettability measurements...

• psRNATarget

• Referenced in 1 article [sw34140]
• target analysis server, which features two important analysis functions: (i) reverse complementary matching between small ... psRNATarget server is designed for high-throughput analysis of next-generation data with an efficient...

• ESpritz

• Referenced in 1 article [sw16911]
• Both a web server for high-throughput analysis and a Linux executable version of ESpritz...

• alsace

• Referenced in 1 article [sw26727]
• package and adds functionality for high-throughput analysis, including definition of time windows, clustering...

• FASTAptamer

• Referenced in 1 article [sw28242]
• FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections. High-throughput sequence...

• THEA

• Referenced in 2 articles [sw20344]
• data are quantified, normalized and classified, the analysis phase is essentially a manual and subjective ... knowledge. RESULTS: THEA (Tools for High-throughput Experiments Analysis) is an integrated information processing system...

• ProbCD

• Referenced in 5 articles [sw20338]
• enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations ... deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic ... package to deal with probabilistic categorical data analysis, ProbCD, that does not require a static ... enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques...

• ConsensusPathDB

• Referenced in 6 articles [sw29342]
• with tools for visualization, analysis and interpretation of high-throughput expression data in the light...

• NEEP

• Referenced in 1 article [sw36005]
• estimated p-values for high-throughput molecular survival analysis. Null Empirically Estimated P-values ... NEEP) is a non-parametric, high-throughput survival analysis meant for molecular expression data...

• GENEVESTIGATOR

• Referenced in 2 articles [sw38837]
• High-throughput gene expression analysis has become a frequent and powerful research tool in biology...

• methylKit

• Referenced in 5 articles [sw23479]
• package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package...

• SeqMap

• Referenced in 6 articles [sw17145]
• essential to the analysis of data from ultra high-throughput sequencing machines. With a carefully...