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 last year
Alternatives and similar repositories for seq2HLA
Users that are interested in seq2HLA are comparing it to the libraries listed below
Sorting:
- ☆117Updated last year
- A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …☆68Updated 3 weeks ago
- nextNEOpi: a comprehensive pipeline for computational neoantigen prediction☆76Updated last month
- Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)☆74Updated last year
- ☆74Updated 3 months ago
- Fast and accurate in silico inference of HLA genotypes from RNA-seq☆138Updated 11 months ago
- Genomic Identification of Significant Targets in Cancer (GISTIC), version 2☆52Updated 3 years ago
- Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data☆43Updated 7 months ago
- Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data☆67Updated 5 years ago
- Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.☆111Updated 10 months ago
- optimization of ribosome P-site positioning in ribosome profiling data☆52Updated 5 months ago
- Estimate locus specific human LINE-1 expression.☆36Updated 2 years ago
- Probabilistic model for inferring clonal population structure from deep NGS sequencing.☆104Updated 4 years ago
- Public repository containing research code for the TCGA PanCanAtlas Splicing project☆41Updated 4 years ago
- A toolset for profiling alternative splicing events in RNA-Seq data.☆81Updated 6 months ago
- Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.☆110Updated 8 months ago
- EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.☆59Updated 7 months ago
- Full-length transcriptome splicing and mutation analysis☆83Updated last year
- REDItools are python scripts to investigate RNA editing at genomic scale.☆67Updated last week
- HMMRATAC peak caller for ATAC-seq data☆99Updated 8 months ago
- ☆38Updated 5 years ago
- ☆87Updated 2 weeks ago
- Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…☆74Updated 2 years ago
- A tool for the calculation of RNA-editing index for RNA seq data☆43Updated last year
- Notes on ChIP-seq and other-seq-related tools☆26Updated last week
- Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19☆76Updated last year
- Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).☆52Updated 3 years ago
- An R package to time somatic mutations☆62Updated 4 years ago
- Tutorial Website☆59Updated 4 years ago
- ☆69Updated 2 years ago