195 skills found · Page 1 of 7
zengxiaofei / HapHiCHapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
B-UMMI / ChewBBACABSR-Based Allele Calling Algorithm
secastel / Phaserphasing and Allele Specific Expression from RNA-seq
bmvdgeijn / WASPWASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
huangnengCSU / LongcallRlongcallR is a tool for SNP calling, haplotype phasing, and allele-specific analysis with long-read RNA-seq data.
immunogenomics / HLA Analyses TutorialA thorough tutorial on HLA imputation and association, accompanying our manuscript "Tutorial: A statistical genetics guide to identifying HLA alleles driving complex disease"
raphael-group / HatchetHATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.
0xTCG / AldyAllelic decomposition and exact genotyping of highly polymorphic and structurally variant genes
10XGenomics / ScHLAcountCount HLA alleles in single-cell RNA-seq data
FelixKrueger / SNPsplitAllele-specific alignment sorting
KalinNonchev / GnomAD DBScalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and WES.
TRON-Bioinformatics / Seq2HLAIn-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.
raphael-group / CalicoSTInferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
cancerit / AlleleCountSupport code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
Michael-Sebero / Genetic Trait DetectorThis python script detects known traits in raw human genetic data.
natsuhiko / RasqualRobust Allele Specific Quantification and quality controL
gxiaolab / ScAlleleNo description available
Kingsford-Group / KouramiKourami: Graph-guided assembly for HLA alleles
pughlab / BamgineerBamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
single-cell-genetics / XCloneDetection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.
