All software used or developed by the ENCODE Consortium
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Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. Publication available at: doi: 10.1093/bioinformatics/btw336
GEM-Tools is a C API and a Python module to support and simplify usage of the GEM Mapper.
chromVar — source
chromVAR is an R package for the analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data.
bioraddbg ATAC-seq MACS2 — source
This Docker container provides an easy to use Docker interface to MACS2 for peak calling with settings tailored for Bio-Rad Single Cell ATAC-seq chemistry.
bioraddbg ATAC-seq filter beads — source
This Docker container provides an easy to use Docker interface to a bead filtration tool with settings tailored for Bio-Rad Single Cell ATAC-seq chemistry. This container takes in .BAM files and performs "knee calling" to compute a bead barcode whitelist and jaccard index threshold for bead-to-droplet merging.
bioraddbg ATAC-seq BWA — source
This Docker container provides an easy to use Docker interface to the BWA alignment tool with settings tailored for Bio-Rad ATAC-Seq chemistry.
guppy_basecaller — source
Ont-Guppy is a basecalling software available to Oxford Nanopore customers. For more information, please see https://nanoporetech.com/
polyAsite_workflow — source
Pipeline to infer poly(A) site clusters through processing of 3' end sequencing libraries prepared according to various protocols.
gencode_utr_fix — source
This package fixes UTR features in the third columns of Gencode GTF by converting UTR annotation into five_prime_utr and three_prime_utr similar to Ensembl.
pyfaidx — source
This python module implements pure Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index.
seqkit — source
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
STARsolo — source
STARsolo is a tool for mapping, demultiplexing, and quantification for single cell RNA-seq.
HTSlib — source
A C library for reading/writing high-throughput sequencing data
ArchR — source
R package for single-cell ATAC-seq data analysis
Scanpy — source
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing.
Seurat — source
Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
split-pipe — source
The Parse Biosciences computational pipeline is an out-of-the-box software tool that you can run locally to convert fastq files straight to processed data (including gene-cell count matrices). Customers purchasing the Whole Transcriptome Kit will receive access to the Parse computational pipeline.
PINTS — source
Yu lab repository for signal generation and peak calling scripts
dREG — source
Detecting Regulatory Elements using GRO-seq and PRO-seq
bigWigMerge — source
This tool from kentUtils merges together multiple bigWigs into a single output
PRINSEQ Lite — source
PRINSEQ will preprocess genomic or metagenomic sequence data in FASTA or FASTQ format
sQTLseekeR — source
sQTLseekeR is a package to detect splicing QTLs (sQTLs), which are variants associated with change in the splicing pattern of a gene. In sQTLSeeker, splicing patterns are modeled by the relative expression of the transcripts of a gene. The most recent version of sQTLseekeR can be employed to detect genetic variant associated to any multivariate phenotypeSoftware type: