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EAGLE / Environment-ASE through Generalized LinEar modeling
Improves power, model and account for over-dispersion inherent in RNA-seq data. EAGLE provides a flexible framework for modeling influence of both technical and biological factors while accounting for extra-binomial variation in sequencing data. This R package is a method to test for gene-environment (GxE) interactions using allele specific expression (ASE). It uses a binomial generalized linear mixed model (GLMM), predicting the relative number of RNA-seq reads from each allele at exonic, heterozygous loci under different environmental conditions.
TACO / Transcriptome Assemblies Combined into One
Reconstructs a consensus transcriptome from a collection of individual assemblies. TACO is an algorithm that employs change point detection to break apart complex loci and correctly delineate transcript start and end sites, and a dynamic programming approach to assemble transcripts from a network of splicing patterns. It also contains an easy to use companion tool for comparing meta-assemblies to reference transcriptomes, assessing overlap with reference and also protein coding potential.
LaSSO / Lariat Sequence Site Origin
Identifies branch points in complex genomes. LaSSO is an algorithm that provides an approach to detect lariat intermediates and to map branch points on a genomic scale. This tool can perform on the identification of additional cryptic or alternative splice sites in analyzing an intronic sequence with its corresponding upstream or downstream exon sequence. Moreover, it can be applied to spot novel splicing events by partitioning the genome with a sliding window while ignoring known annotations.
PAQR / Polyadenylation Site Usage Quantification From RNA Sequencing Data
New
Infers relative poly(A) site used in terminal exons from RNA sequencing data and KAPAC. PAQR is composed of three modules: (1) a script to deduce transcript integrity values, (2) a script to create the coverage profiles for all considered terminal exons, and (3) a script to obtain the relative usage together with the estimated expression of poly(A) sites with sufficient evidence of usage. The software enables evaluation of 3′ end processing in data sets such as those from The Cancer Genome Atlas (TCGA).
KAPAC / k-mer activity on polyadenylation site choice
New
Infers sequence motifs that are associated with the processing of poly(A) sites in specific samples. KAPAC is an approach that deduces position-dependent activities of sequence motifs on 3′ end processing from changes in poly(A) site usage between conditions. The software analysis of TCGA data reveals pyrimidine-rich elements associated with the use of poly(A) sites in cancer and implicates the polypyrimidine tract-binding protein 1 (PTBP1) in the regulation of 3′ end processing in glioblastoma.
GISPA / Gene Integrated Set Profile Analysis
Allows identification of multiple gene sets that play a role in the characterization, clinical application, or functional relevance of a disease phenotype. GISPA is designed to characterize the molecular tumor profile of a single sample relative to other, comparison samples based on changes (increasing/decreasing) among several diverse, genome-wide data types. A user-friendly interface, shinyGISPA, was also developed to combine and compare multiple levels of genomic to proteomic data.
FocalScan
A tool designed to simultaneously uncover patterns of focal copy number alteration and coordinated expression change, thus combining both principles. FocalScan outputs a ranking of tentative cancer drivers or suppressors. FocalScan works with RNA-seq data, and unlike other tools it can scan the genome unaided by a gene annotation, enabling identification of novel putatively functional elements including lncRNAs. Application on a breast cancer data set suggests considerably better performance than other DNA/RNA integration tools.
Barnacle / Browsing Assembled RNA for Chimeras with Localized Evidence
Resolves conflicts due to repeated sequences in RNA. Barnacle is a pipeline for detecting and characterizing chimeric transcripts from long RNA sequences, such as those generated by de novo transcriptome assembly. It identifies sequences with a variety of anomalous alignment topologies, predicts partial tandem duplications (PTDs), internal tandem duplications (ITDS), and fusions from these sequences, and measures the coverage of the inferred chimeric transcripts relative to corresponding wild-type transcripts.
SPEQC / Structure Probing Experiment Quality Control
Rapid and quantitative metrics for evaluating structure probing data quality. SPEQC uses metrics to rapidly and quantitatively evaluate data quality from structure probing experiments, demonstrating their efficacy on both small synthetic libraries and transcriptome-wide datasets. A signal-to-noise ratio concept evaluates replicate agreement, which has the capacity to identify high-quality data. The developed metrics and tools will be useful in summarizing large-scale datasets and will help standardize quality control in the field.
RNASeq-er
Accesses the results of a systematically and continually updated and continually growing analysis of public RNA-seq data in European Nucleotide Archive (ENA). RNASeq-er enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices as well as sample attributes annotated with ontology terms. It provides access to baseline gene expression quantifications, aggregated across all runs in each of over 4000 normal tissue, cell type, developmental stage, sex, and strain conditions in 61 species.
TcellClonality
An R script for processing MiTCR-derived CDR3 data from Peripheral T Cell Lymphoma (PTCL) RNA-seq. TcellClonality will remove non-productive CDR3 sequences, calculate the relative abundance of each CDR3, resolves ambiguity in CDR3 chain assignment, and classifies CDR3 clonotypes as being dominant or background (using control samples to determine the background level). It then calculates Shannon Entropy and estimates Tumor Purity for each sample. Finally, it includes code for analyzing T Cell Receptor (TCR) C gene expression. For analysis, RSEM v1.2.29 was used to calculate gene expression levels for all transcripts, and transcripts from TCR C genes were extracted.
V'DJer
A software for inference of B-cell receptor (BCR) repertoires using short-read RNA sequencing data. V'DJer uses customized read extraction, assembly and V(D)J rearrangement detection and filtering to produce contigs representing the most abundant portions of the BCR. V’DJer allows for full inference of repertoire characteristics including variable and joining gene segment usage, population diversity, sequence sharing between populations, antigen binding region amino acid properties and motifs, clonal structure and somatic hypermutation in BCR repertoires.
EVtransfer
Allows study of extracellular vesicle (EV) mediated mRNA transfers between cells. EVtransfer also investigates the role of exosomes as a vehicle in mediating the exchange. The software enables quality control, alignment, mapping, and base call recalibration on the raw SNP array and RNA sequencing reads data, evaluation of the significance of genotypic variation of a cell line under in vitro co-culture, and estimation of the rate of false discovered loci involving in the transfer process.
ToNER / Transformation of Nucleotide Enrichment Ratios
Identifies enriched sites from differential RNA-seq experiments comprising enriched and unenriched libraries. ToNER uses a global distribution model to report statistics of enrichment for all nucleotides. It calculates position-wise normalized read depth ratio between two libraries for all mapped genome positions. The tool is able to identify transcription start site (TSS) from Cappable-seq data in prokaryotes. It can locate enriched positions in complex data of eukaryotes such as m6A-seq.
HapIso / Haplotype-specific Isoform Reconstruction
Reconstructs the haplotype-specific isoforms from long single-molecule reads. HapIso is a comprehensive method for the accurate reconstruction of the haplotype-specific isoforms of a diploid cell that uses the splice mapping of the long single-molecule reads and partitions the reads into parental haplotypes. To overcome gapped coverage and splicing structures of the gene, the haplotype reconstruction procedure is applied independently for regions of contiguous coverage defined as transcribed segments.
DAFS
A data-adaptive approach was developed to estimate the lower bound of high expression for RNA-seq data. The Kolmgorov-Smirnov statistic and multivariate adaptive regression splines were used to determine the optimal cutoff value for separating transcripts with high and low expression. Results from the proposed method were compared to results obtained by estimating the theoretical cutoff of a fitted two-component mixture distribution. The robustness of the proposed method was demonstrated by analyzing different RNA-seq datasets that varied by sequencing depth, species, scale of measurement, and empirical density shape.
TABASCO
Allows genome-scale simulation of transcription and translation at individual molecule and single base-pair resolution. TABASCO is a single-molecule stochastic simulator optimized to handle molecular events specific to gene expression such as the initiation, elongation and termination of transcription and translation as well as interactions among protein-DNA complexes. The software provides the descriptions of gene expression dynamics while allowing analysis of phenomena such as how intermolecular events between DNA-protein complexes affect system-wide gene expression.
phASER / phasing and Allele Specific Expression from RNA-seq
A fast and accurate approach for phasing variants that are overlapped by sequencing reads, including those from RNA-sequencing (RNA-seq), which often span multiple exons due to splicing. phASER provides 1) dramatically more accurate phasing of rare and de novo variants compared to population-based phasing; 2) phasing of variants in the same gene up to hundreds of kilobases away which cannot be obtained from DNA-sequencing reads; 3) high confidence measures of haplotypic expression, greatly improving power for allelic expression studies.
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Sequins / Sequencing spike-ins
A set of spike-in RNA standards that represent full-length spliced mRNA isoforms. Sequins have an entirely artificial sequence with no homology to natural reference genomes, but they align to gene loci encoded on an artificial in silico chromosome. The combination of multiple sequins across a range of concentrations emulates alternative splicing and differential gene expression, and it provides scaling factors for normalization between samples. Sequins are an easy, simple and effective approach to assess the NGS workflow, calculate diagnostic statistics, internal reference ladders and normalize between multiple samples.
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