shahcompbio / hmmcopy_utilsLinks
Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.
☆41Updated 4 years ago
Alternatives and similar repositories for hmmcopy_utils
Users that are interested in hmmcopy_utils are comparing it to the libraries listed below
Sorting:
- Enhanced version of the FastQTL QTL mapper☆70Updated 2 years ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆67Updated 6 years ago
- QDNAseq package for Bioconductor☆53Updated last year
- TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C☆113Updated 4 years ago
- ☆38Updated 4 years ago
- ☆49Updated 2 years ago
- DCC/DAC methylation pipeline source☆57Updated 5 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 6 years ago
- Allele-specific alignment sorting☆60Updated 2 years ago
- GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.☆44Updated 8 years ago
- Software to compute reproducibility and quality scores for Hi-C data☆50Updated 6 years ago
- ENCODE long read RNA-seq pipeline☆51Updated 2 years ago
- tools to find circRNAs in RNA-seq data☆44Updated 8 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆98Updated 4 years ago
- ☆54Updated 2 years ago
- SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3☆38Updated 5 years ago
- phasing and Allele Specific Expression from RNA-seq☆116Updated last year
- ENCODE whole-genome bisulfite sequencing (WGBS) pipeline☆32Updated 3 years ago
- Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…☆77Updated 2 years ago
- Tools for processing and analyzing structural variants.☆33Updated 10 years ago
- Tutorial Website☆60Updated 4 years ago
- SingleCell Nanopore sequencing data analysis☆61Updated 5 months ago
- BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.☆28Updated 6 years ago
- A method for circular DNA detection based on probabilistic mapping of ultrashort reads☆66Updated last year
- ☆72Updated 2 years ago
- ☆21Updated last month
- SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …☆51Updated last month
- code associated with crane-nature-2015, 10.1038/nature14450☆36Updated 10 years ago
- ☆13Updated 8 years ago
- Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools☆81Updated 4 years ago