All software used or developed by the ENCODE Consortium
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seqFISH+ — sourcePipeline to process seqFISH data.
Software type: quantification, other
CRISPy — sourceCRISPy is a lightweight versatile pipeline for CRISPR-screening analysis.
Software type: quantification
RELICS — sourceRELICS is an analysis method for discovering functional sequences from tiling CRISPR screens.
Software type: quantification
MPRAmodel — sourceTool to analyze counts and generate processed files
Software type: quantification, file format conversion
MPRAcount — sourceTool to process Tag-seq data and generate the count matrix
Software type: quantification
Library sequencing match — sourceHouse script that was matching the guides (from an input list) to the fastq files as returned by deep sequencing
Software type: quantification
Stratified LD fourth moments (S-LD4M) — sourceThis software implements our Stratified LD 4th moments regression (S-LD4M) method for estimating polygenicity across allele frequencies and functional categories, as described in our manuscript “Polygenicity of complex traits is explained by negative selection”.
Software type: quantification
DESeq2 — sourceDifferential gene expression analysis based on the negative binomial distribution
Software type: quantification
CQN — sourceSoftware used to generate GC content and length normalized matrix
Software type: quantification
Salmon — sourceSoftware used to generate transcriptome quantifications
Software type: quantification
Tximport — sourceSoftware used to generate length scaled TPM matrix
Software type: quantification
HTSeq — sourceHTSeq: Analysing high-throughput sequencing data with Python
Software type: quantification
Cuffdiff — sourceCuffdiff can be used to find significant changes in transcript expression, splicing, and promoter use.
Software type: quantification
Miso — sourceMISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples
Software type: quantification
rMATs — sourceMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.
Software type: quantification
DESeq — sourceDESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression.
Software type: quantification