Builds transcriptomes from RNA-seq data. Trinity is a standalone software composed of three main components: (i) Inchworm, that first generates transcript contigs; (ii) Chrysalis, for clustering them and constructing complete de Bruijn graphs for each cluster and; (iii) Butterfly that processes individual graphs in parallel for finally resulting to the reconstruction of the transcript sequences.
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Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. Cufflinks assembles individual transcripts from RNA-seq reads that have been aligned to the genome. This software is able to infer the splicing structure of each gene because reads from multiple splice variants for a given gene can be found in a sample. Quantification of transcript abundances is also possible by preferring a reference annotation to assembling the reads.
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.
Identifies differentially expressed genes or isoforms for RNA-seq data from different samples. DEGseq encourages users to export gene expression values in a table format which could be directly processed by edgeR. It is based on the random sampling model which fits well the random sampling model. This tool can be applied to recognize differential expression of exons or pieces of transcripts.
Allows users to handle RNA-sequencing pipeline based on the TopHat, Cufflinks and CummeRbund suite of software. Tuxedo is a program that enables assessment of alternative splicing (AS) inferred on fragments per kilobase per million (FPKM) values. It can assist researchers to detect genes and splicing variants and compare gene expression and transcripts under different conditions.
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Discover our proposed protocols.
They are easy to use or edit to meet your needs.
They are easy to use or edit to meet your needs.
Induction of endogenous retroelements as a potential mechanism for mouse specific drug induced carcinogenicity
Tools (5):
STAR, SAMtools, Cufflinks, Spanki, BEDTools
Topics (6):
sRNA-seq analysis, RNA-seq analysis, Mus musculus, Liver Neoplasms, Digestive System Neoplasms, Neoplasms
Computational Evidence of NAGNAG Alternative Splicing in Human Large Intergenic Noncoding RNA
Tools (4):
TopHat, SAMtools, nagnag, Biostrings
Topics (1):
RNA-seq analysis
Gene expression profiling of U2AF2 dependent RNA protein interactions during CD4 + T cell activation
Tools (3):
GO-Elite, AltAnalyze, WikiPathways
Topics (5):
Transcription analysis, sRNA-seq analysis, Gene expression microarray analysis, DNA methylation array analysis, RNA-seq analysis
FUS/TLS acts as an aggregation dependent modifier of polyglutamine disease model mice
Tools (4):
GeneSpring GX, AltAnalyze, FIRMA, DAVID
Topics (1):
Gene expression microarray analysis
Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles
Tools (6):
SUPPA, Splicing Express, CLC Genomics Workbench, STAR, RSEM, DESeq2
Topics (3):
sRNA-seq analysis, RNA-seq analysis, Metatranscriptomic sequencing analysis