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Results for « RNA sequencing »

URSM / Unified RNA-Sequencing Model
Analyzes two types of RNA-seq: single cell data and bulk data. URSM adjusts dropout events in single cell data and achieves simultaneously deconvolution in bulk data. This software doesn’t need to calculate on the same subjects the single cell and bulk data. It can (1) obtain reliable estimation of cell type specific gene expression profiles; (2) infer the dropout entries in single cell data; and (3) infer the mixing proportions of different cell types in bulk samples.
PAQR / Polyadenylation Site Usage Quantification From RNA Sequencing Data
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).
CONICS / COpy-Number analysis In single-Cell RNA-Sequencing
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Identifies large-scale copy-number variants (CNVs) in scRNA-seq. CONICS provides a method to separate neoplastic cells for downstream analysis. It includes algorithms to triage cells from a scRNA-seq assay, based on the presence of CNVs detected in an orthogonal DNA sequencing experiment. It integrates tumor-normal fold-changes with the minor-allele frequencies of point mutations to estimate false-discovery rates (FDRs) in CNV classification. Additionally, it includes routines to perform downstream phylogeny assessment and gene co-expression analysis.
Bowtie
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Aligns short read geared toward mammalian re-sequencing. Bowtie is based on a Burrows-Wheeler index based on the full-text minute-space (FM) index. It follows two steps: an initial, ungapped seed-finding stage that derives advantage from the speed and memory efficiency of the full-text minute index and a gapped extension stage that employs dynamic programming and benefits from the efficiency of single-instruction multiple-data (SIMD) parallel processing available on modern processors.
FUCHS / FUll CHaracterization of circular RNA using RNA Sequencing
Characterizes circRNAs candidates. FUCHS provides the user with directions for further steps to investigate the circRNA’s function and biogenesis. FUCHS is able to identify alternative exon usage within the same circle boundaries, summarize the different circles emerging from the same host-gene, quantify double-breakpoint fragments as indicator for circularity and visualize a circRNA’s read coverage profile independent of any genome browser.
GATK / Genome Analysis ToolKit
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Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and ables to support projects of any size. The application compiles an assortment of command line allowing one to analyze of high-throughput sequencing (HTS) data in various formats such as SAM, BAM, CRAM or VCF. The website includes multiple documentation for guiding users.
DAVID / Database for Annotation, Visualization and Integrated Discovery
Allows users to obtain biological features/meaning associated with large gene or protein lists. DAVID can determine gene-gene similarity, based on the assumption that genes sharing global functional annotation profiles are functionally related to each other. It groups related genes or terms into functional groups employing the similarity distances measure. This tool takes into account the redundant and network nature of biological annotation contents.
GSEA / Gene Set Enrichment Analysis
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Evaluates microarray data at the level of gene sets. GSEA aims to determine whether members of a gene set S tend to occur toward the top (or bottom) of the list L, in which case the gene set is correlated with the phenotypic class distinction. This method eases the interpretation of a largescale experiment by identifying pathways and processes, and can boost the signal-to-noise ratio when the members of a gene set exhibit strong cross-correlation, allowing to detect modest changes in individual genes.
find_circ
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Detects head-to-tail spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) in RNA-seq data. find_circ is a pipeline that can find circRNAs in any genomic region. It takes advantage of long (,100 nucleotides) reads, and predicts the acceptor and donor splice sites used to link the ends of the RNAs. This method provides evidence that circRNAs form an important class of post-transcriptional regulators.
DESeq
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Performs differential gene expression analysis. DEseq is a method that integrates methodological advances with features to facilitate quantitative analysis of comparative RNA-seq data using shrinkage estimators for dispersion and fold change. The software is suitable for small studies with few replicates as well as for large observational studies. Its heuristics for outlier detection assist in recognizing genes for which the modeling assumptions are unsuitable and so avoids type-I errors caused by these.
SAMtools
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Allows users to interact with high-throughput sequencing data. SAMtools permits the manipulation of alignments in the SAM/BAM/CRAM formats: reading, writing, editing, indexing, viewing and converting SAM/BAM/CRAM format. It limits the mapping quality of reads with excessive mismatches and applies base alignment quality to fix alignment errors. This tool can sort and merge alignments, remove polymerase chain reaction (PCR) duplicates or generate per-position information.
Seurat
Allows studying of spatial patterning of gene expression at the single-cell level. Seurat is an R package that enables quality control (QC), analysis, and exploration of single cell RNA-seq data. The software includes three computational methods: (1) unsupervised clustering and discovery of cell types and states, (2) spatial reconstruction of single cell data, and (3) integrated analysis of single cell RNA-seq across conditions, technologies, and species. It can also localize rare subpopulations, and map both spatially restricted and scattered groups.
TopHat
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Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie. TopHat also analyzes the mapping results to identify splice junctions between exons. It can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. The tool combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes.
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Results for « RNA sequencing »

GWIPS-viz / Genome Wide Information on Protein Synthesis visualized
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Provides access to the genomic alignments of public ribo-seq reads in conjunction with mRNA-seq reads along with relevant annotation tracks. GWIPS-viz is a specialized ribo-seq browser allowing researchers to support ribo-seq evidence for alternative proteoforms inferred from phylogenetic analysis or detect with proteomics or other experimental techniques. It can be used as a support tool for predictions based on other approaches and for generating hypotheses that can be tested using methods other than ribo-seq.
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.
Anolis carolinensis
A database which offers gene annotation of Anolis carolinensis also known as Carolina anole an arboreal lizard. The anole lizard genome is composed of 13 chromosomes, assembled from 41.9861 contigs and 2.143 scaffolds. The total number of bases in the genome is 1.78Gb. The gene set for anole lizard was built using the Ensembl genebuild pipeline. In addition to the main set, gene models have been predicted for each tissue type using the RNA-Seq pipeline. Anolis carolinensis belongs to the Dactyloidae family.
DeepBind
An approach based on deep convolutional neural networks. DeepBind can discover new patterns even when the locations of patterns within sequences are unknown—a task for which traditional neural networks require an exorbitant amount of training data. DeepBind addresses the above challenges: (i) It can be applied to both microarray and sequencing data; (ii) it can learn from millions of sequences through parallel implementation on a graphics processing unit (GPU); (iii) it generalizes well across technologies, even without correcting for technology-specific biases; (iv) it can tolerate a moderate degree of noise and mislabeled training data; and (v) it can train predictive models fully automatically, alleviating the need for careful and time-consuming hand-tuning.
starBase
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Provides resources to decode Pan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq data and tumor samples. starBase deciphers Protein-RNA and miRNA-target interactions, such as protein-lncRNA, protein-sncRNA, protein-mRNA, protein-pseudogene, miRNA-lncRNA, miRNA-mRNA, miRNA-circRNA, miRNA-pseudogene, miRNA-sncRNA interactions and ceRNA networks from 108 CLIP-Seq datasets.
Expression Atlas
Provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. Expression Atlas consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Expression Atlas search interface allows for querying one or more genes or proteins from a selected species. The user can also add search filters for sample attributes and experimental factors, taking full advantage of ontology-driven query expansion.
The Apple Genome and Epigenome
Gives access to the apple genome. The Apple Genome and Epigenome contains up to date gene annotation, transposable element (TE) annotation, genetic markers, DNA methylation data, small RNA data and microarray probes. The genome was obtained using a homozygous apple variety (a doubled haploid of ‘Golden Delicious’) and by combining several sequencing and mapping technologies. The reference apple genome sequence offers insights into the genome dynamics of a tree and provides a basis for future studies.
ChimerDB
Offers fusion genes encompassing analysis of deep sequencing data and manual curations. ChimerDB is composed of three modules: ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. RNA-Seq data of The Cancer Genome Atlas (TCGA) project covering 4569 patients in 23 cancer types were analysed using two reliable programs of FusionScan and TopHat-Fusion. The user interface supports diverse search options and graphic representation of fusion gene structure.
AtCircDB
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Provides a comprehensive and tissue-specific plant circular RNA database. AtCircDB is an online resource for predicted and validated Arabidopsis hosting circular RNA candidates identified from largescale sequencing data. This database currently hosts four categories of information: (i) circular RNA information, (ii) potential miRNA–circular RNA interaction, (iii) super circular region and (iv) tissue information.
AtRTD / Arabidopsis Thaliana Reference Transcript Dataset
Provides a comprehensive high-quality reference transcript dataset about Arabidopsis transcripts. AtRTD contains more than 82 190 unique transcript models. It was generated by integration of transcript assemblies of ca. 8.5 billion pairs of reads from 285 RNA-seq data sets obtained from 129 RNA-seq libraries. The database contains 37 137 events and those which occurred at least 50 times made up 95.24% of all alternative splicing events.
RISE / RNA Interactome from Sequencing Experiments
Provides RNA-RNA interactions (RRIs) identified through high-throughput sequencing technologies. RISE is a comprehensive database of RNA interactome from sequencing experiments. It includes (i) comprehensive curation of RRIs, (ii) a large dataset of RRIs among mRNAs and lncRNAs, (iii) details of the interacting sites and (iv) extensive annotations for each RRI. It provides an assistance for researchers looking for interaction and other functional information on individual RNAs, and analyzing RRI networks of specific pathways or systems.
ISOexpresso
Facilitates expression-based isoform-level analysis of large-scale TCGA (The Cancer Genome Atlas) multi-cancer RNA-seq data. ISOexpresso is a database which provides information regarding isoform existence and expression, which can be grouped by cancer vs. normal conditions, cancer types, and tissue types. It implements two main functions: the Isoform Expression View function creates visualizations for condition-specific RNA/isoform expression patterns upon query of a gene of interest and the User Data Annotation function supports annotation of genomic variants to determine the most plausible consequence of a variation among many possible interpretations.
RNA-Seq Atlas
A web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression profiles and tools to both compare tissues and find genes with specific expression patterns. To enlarge the scope of the RNA-Seq Atlas, the data were linked to common functional and genetic databases, in particular offering information on the respective gene, signaling pathway analysis and evaluation of biological functions by means of gene ontologies. Additionally, data were linked to several microarray gene profiles, including BioGPS normal tissue profiles and NCI60 cancer cell line expression data. Our data search interface allows an integrative detailed comparison between our RNA-Seq data and the microarray information.
ChiTaRS
Offers chimeric transcripts and RNA-seq matched with protein-protein interactions. ChiTaRS database is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in. The database comprises 34922 chimeric transcripts along with 11714 cancer breakpoints, from eight organisms, and includes the manual annotation of 200 sense-antiSense (SaS) chimeras. Multiple cross-references to GeneCards, iHop, PubMed, NCBI, Ensembl, OMIM, RefSeq and the Mitelman collection are included for every entry in the ‘Full Collection’. For every chimera, a predicted chimeric protein-protein interaction (ChiPPI) network has been added. It allows for easy visualization of protein partners of both parental and fusion proteins for all human chimeras.
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Results for « RNA sequencing »

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