andrej-fischer / cloneHDLinks
High-definition reconstruction of clonal composition from next-generation sequencing data
☆40Updated 9 years ago
Alternatives and similar repositories for cloneHD
Users that are interested in cloneHD are comparing it to the libraries listed below
Sorting:
- Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model☆27Updated last year
- Multi-sample cancer phylogeny reconstruction☆35Updated 7 years ago
- Tools to handle reads sequenced with unique molecular identifiers (UMIs).☆30Updated 8 years ago
- highly-efficient & lightweight mutation signature matrix aggregation☆19Updated 3 years ago
- fast webservices based query tool for large sets of genomic features☆25Updated last month
- FermiKit small variant calls for public SGDP samples☆17Updated 8 years ago
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated 2 years ago
- Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.☆23Updated 6 years ago
- Chromatin segmentation in R☆19Updated 7 years ago
- Scripts and software supplement for "Gene-level differential analysis at transcript-level resolution" by Yi, Pimentel, Bray and Pachter☆19Updated 7 years ago
- Expectation-Maximization algorithm for Allele-Specific Expression☆21Updated 2 years ago
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆49Updated 6 years ago
- Python package and routines for merging VCF files☆29Updated 4 years ago
- a parallel R package for detecting copy-number alterations from short sequencing reads☆23Updated 3 years ago
- BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants☆24Updated 9 years ago
- A tool for Read Multi-Mapper Resolution☆23Updated 8 years ago
- A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.☆26Updated 8 years ago
- Run Picard on BAM files and collate 90 metrics into one file.☆41Updated 7 years ago
- Sashimi plots for RNA-seq data using detected transcripts☆28Updated 3 months ago
- QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.☆32Updated 9 years ago
- Relative Abundance of Transcripts: An R package for the detection of Differential Transcript isoform Usage.☆34Updated 3 years ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆42Updated 3 years ago
- Keep Me Around: Intron Retention Detection☆29Updated 6 years ago
- A small R package to make sequencing read coverage plots in R.☆38Updated 3 years ago
- Flexible Bayesian inference of mutational signatures☆35Updated 2 years ago
- The SomaticSignatures package offers the framework for identifying mutational signatures of single nucleotide variants (SNVs) from high-t…☆22Updated 5 years ago
- Response to blog post about Salmon☆37Updated 7 years ago
- CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.☆29Updated 4 years ago
- Modeling and correcting fragment sequence bias for RNA-seq☆24Updated last year
- An awk-like VCF parser☆56Updated last year