Purpose in project
Showing 25 of 176 results
SoftwarereleasedSoftware package for analysis of Hi-C data.
SoftwarereleasedJuicer is a platform for analyzing high-resolution Hi-C data.
SoftwarereleasedConverts dbGaP-protected raw data in sra format to fastq format.
SoftwarereleasedPython module warapping htslib C-API and samtools for accessing sam formatted alignment filesSoftware type: other
SoftwarereleasedGenerates normalized density signal from aligned and filtered reads for DNase ENCODE uniform processing pipeline.Software type: file format conversion
SoftwarereleasedEvaluates a sample of paired or single-end aligned and filtered reads for DNase ENCODE uniform processing pipeline.Software type: quality metric
SoftwarereleasedSignal generation for long-RNA-seq ENCODE uniform processing pipeline.Software type: file format conversion
SoftwarereleasedMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design.
SoftwarereleasedBowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
SoftwarereleasedProvides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
SoftwarereleasedLong Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants. These pipelines combine Chromium-specific algorithms with widely used components such as BWA, Freebayes, and GATK. Output is delivered in standard BAM, VCF, and BEDPE formats that are augmented with long range information.Software type: aligner, variant annotation