Showing 25 of 29 results

• Software

  released

  RNA-seq quantification: eQTL-Catalogue/rnaseq — source

  RNA-seq quantification: eQTL-Catalogue/rnaseq. nfcore/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data.

  Software type: quantification

• Software

  released

  rampage-mad-qc — source

  Mean Absolute Deviation (MAD) and correlation calculated from two replicates for Rampage ENCODE uniform processing pipeline.

  Software type: quality metric

• Software

  released

  srna-mad-qc — source

  Mean Absolute Deviation (MAD) and correlation calculated from two replicates for small-RNA-seq ENCODE uniform processing pipeline.

  Software type: quality metric

• Software

  released

  lrna-signals-stranded — source

  Signal generation from stranded alignments for long-RNA-seq ENCODE uniform processing pipeline.

  Software type: file format conversion

• Software

  released

  srna-signals — source

  Signal generation for small-RNA-seq ENCODE uniform processing pipeline.

  Software type: file format conversion

• Software

  released

  RNA pipelines — source

  Repository of all RNA-seq (long-, small-, and rampage) ENCODE Uniform processing pipelines.

• Software

  released

  rampage-peaks — source

  Peak calling by GRIT for Rampage ENCODE uniform processing pipeline.

  Software type: peak caller

• Software

  released

  FusionSeq — source

  A computational framework that detects chimeric transcripts from paired-end RNA-seq experiments.

  Software type: transcript identification

• Software

  released

  Flux Capacitor — source

  A program to estimate the frequencies of annotated transcripts (GTF format) from an RNA-Seq experiment, solving a linear program inferred from the observed read mappings (BAM format). There are options for single, stranded, and/or paired-end reads.

• Software

  released

  Scripture — source

  Reconstructs transcriptomes, relying solely on RNA-seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has module

  Software type: transcriptome assembly

• Software

  released

  lrna-mad-qc — source

  Mean Absolute Deviation (MAD) and correlation calculated from two replicates for long-RNA-seq ENCODE uniform processing pipeline.

  Software type: quality metric

• Software

  released

  rampage-signals — source

  Signal generation for Rampage ENCODE uniform processing pipeline.

  Software type: file format conversion

• Software

  released

  lrna-index-tophat — source

  Indexing of reference genome by TopHat for long-RNA-seq ECODE uniform processing pipeline.

  Software type: other

• Software

  released

  lrna-index-star — source

  Indexing of reference genome by STAR for long-RNA-seq ECODE uniform processing pipeline.

• Software

  released

  lrna-index-rsem — source

  Indexing of reference genome by RSEM for long-RNA-seq ECODE uniform processing pipeline.

• Software

  released

  RSEQtools — source

  Processes, quantifies, and annotates gene expression data from RNA-seq experiments. Utilizes Mapped Read Format (MRF) for secure and efficient analysis

• Software

  released

  Bowtie — source

  Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint s

• Software

  released

  Median Absolute Deviation — source

  Calculates the Median Absolute Deviation (MAD) and correlation of two gene quantifications from replicate RNA-seq experiments. A measure of reproducibility, inversely correlated with data quality.

  Software type: quality metric

• Software

  released

  RSEM — source

  A software package for estimating gene and isoform expression levels from RNA-Seq data. RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.

  Software type: transcript identification

• Software

  released

  rampage-idr — source

  Irreproducible Discovery Rate (IDR) calculation from two replicates for Rampage ENCODE uniform processing pipeline.

  Software type: quality metric

• Software

  released

  lrna-quantification — source

  Quantification of annotation results by RSEM for long-RNA-seq ENCODE uniform processing pipeline.

  Software type: transcript identification

• Software

  released

  lrna-signals-unstranded — source

  Signal generation from unstranded alignments for long-RNA-seq ENCODE uniform processing pipeline.

  Software type: file format conversion

• Software

  released

  GRIT — source

  Generalized RNA Integration Tool: Transcript prediction utilizing RNA-seq and gene boundary information.

  Software type: peak caller

• Software

  released

  Irreproducible Discovery Rate (IDR) — source

  Measures consistency between replicates in high-throughput experiments. Also uses reproducibility in score rankings between peaks in each replicate to determine an optimal cutoff for significance. The core IDR R package can be downloaded from the IDR do

  Software type: quality metric, filtering

• Software

  released

  IQSeq — source

  Uses RNA-seq data for isoform quantification.