TRON-Bioinformatics / seq2HLALinks
In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.
☆49Updated 2 weeks ago
Alternatives and similar repositories for seq2HLA
Users that are interested in seq2HLA are comparing it to the libraries listed below
Sorting:
- A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …☆68Updated last month
- ☆117Updated last year
- Fast and accurate in silico inference of HLA genotypes from RNA-seq☆139Updated last year
- Public repository containing research code for the TCGA PanCanAtlas Splicing project☆42Updated 4 years ago
- Estimate locus specific human LINE-1 expression.☆36Updated 2 years ago
- ☆75Updated 4 months ago
- Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.☆110Updated 9 months ago
- Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).☆54Updated 3 years ago
- Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)☆74Updated 2 years ago
- Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools☆79Updated 3 years ago
- nextNEOpi: a comprehensive pipeline for computational neoantigen prediction☆76Updated 2 months ago
- mgatk: mitochondrial genome analysis toolkit☆108Updated 7 months ago
- Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)☆62Updated 4 years ago
- ☆38Updated 5 years ago
- Genomic Identification of Significant Targets in Cancer (GISTIC), version 2☆52Updated 3 years ago
- Dynamics analysis of Alternative PolyAdenylation from RNA-seq☆61Updated last year
- REDItools are python scripts to investigate RNA editing at genomic scale.☆68Updated last month
- A tool for the calculation of RNA-editing index for RNA seq data☆43Updated last year
- Full-length transcriptome splicing and mutation analysis☆84Updated last year
- Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.☆111Updated 11 months ago
- A modular, containerized pipeline for ATAC-seq data processing☆58Updated 3 months ago
- Tutorial Website☆59Updated 4 years ago
- Fork of the Polysolver project☆31Updated 5 years ago
- Probabilistic model for inferring clonal population structure from deep NGS sequencing.☆107Updated 5 years ago
- CLIP-seq Analysis of Multi-mapped reads☆31Updated 4 years ago
- Notes on ChIP-seq and other-seq-related tools☆26Updated last month
- HMMRATAC peak caller for ATAC-seq data☆99Updated 9 months ago
- ROSE: RANK ORDERING OF SUPER-ENHANCERS☆51Updated last year
- Links to ATAC-seq analysis tools☆69Updated 3 years ago
- tools to find circRNAs in RNA-seq data☆44Updated 7 years ago