Assists users in mapping reads to a reference genome. Subread offers a suite of programs for processing next-generation sequencing read data. This package includes Subread (an aligner), Subjunc (an aligner), Sublong (a long-read aligner), Subindel (a long indel detection program), featureCounts (a read quantification program), exactSNP (an SNP calling program) and other utility programs.
Simplifies quantitative investigation of comparative RNA-seq data. DESeq2 employs shrinkage estimators for dispersion and fold change. It counts the total number of reads that can be uniquely assigned to a gene. It serves for improved gene ranking and visualization, hypothesis tests above and below a threshold, and the regularized logarithm transformation for quality evaluation and clustering of over-dispersed count data. This version of DESeq uses shrinkage estimators for dispersion and fold change to ease quantitative analysis of comparative RNA-seq data.
Provides a toolbox for genomic analyses on BAM files. BamBam is a package of more than 10 applications intending to assist users in usual tasks including phylogeny inference or differential expression analysis. It includes features to: (i) quantify reads mapped to each gene in a genome; (ii) detect single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) or (iii) summarize read coverage of sequences or regions.
Provides web applications, as well as modular analysis pipelines for high-throughput sequencing (HTS) data analysis. HTSstation workflows rely on interconnected modules revolving around the sequence mapping which uses Bowtie to map sequencing reads to a reference genome or sequence database, and calculates genome-wide coverage profiles. The software offers several applications, such as mapping, analysis of ChIP-seq peaks, a e RNA-seq procedure, modules for 4C-seq and for applying SAMtools pileup to detect discordant bases in reads aligned to a reference genome.
Analyses the chloroplast transcriptome using RNA-Seq. ChloroSeq uses RNA-Seq alignment data to deliver detailed analyses of organelle transcriptomes, which can be fed into statistical software for further analysis and for generating graphical representations of the data. It can also examine splicing efficiency and RNA editing profiles.
Offers a statistical model for counts of RNA-Seq data. mseq is an R package that gathers an iterative glm procedure for the Poisson linear model, a training procedure of the multiple additive regression trees (MART) model and cross-validation for both methods. It can model non-uniformity in short-read rates with the aim of improving the estimation of gene and isoform expressions for both Illumina and Applied Biosystems data.
Consists of a dimension reduction technique designed for complex data sets with multiple overlaid signals observed in noisy conditions. SMSSVD is a parameter-free unsupervised dimension reduction technique primarily designed to reduce noise, adaptively for each low-rank-signal in a data matrix. The software represents the data in a way that enables unbiased exploratory analysis and reconstruction of the multiple overlaid signals, including finding the variables that drive the different signals. It was evaluated on several gene expression and synthetic data sets.