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r-numbat
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public |
A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.
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2025-10-10 |
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orthanq
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public |
Uncertainty aware HLA typing and general haplotype quantification.
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2025-10-10 |
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hybran
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public |
Comparative prokaryotic genome annotation
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2025-10-10 |
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r-hahmmr
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public |
Haplotype-aware Hidden Markov Model for RNA (HaHMMR) is a method for detecting copy number variations (CNVs) from bulk RNA-seq data. Additional examples, documentations, and details on the method are available at <https://github.com/kharchenkolab/hahmmr/>.
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2025-10-10 |
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r-sartools
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public |
Statistical Analysis of RNA-Seq data.
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2025-10-10 |
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concoct
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public |
Clustering cONtigs with COverage and ComposiTion
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2025-10-10 |
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coot-headless
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public |
Coot Headless API - Software for macromolecular model building.
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2025-10-10 |
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atol-qc-raw-ont
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public |
Run read QC on ONT reads.
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2025-10-10 |
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bioconda-repodata-patches
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public |
Generate tweaks to index metadata, hosted separately from anaconda.org index.
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2025-10-10 |
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r-scistreer
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public |
Fast maximum-likelihood phylogeny inference from noisy single-cell data using the 'ScisTree' algorithm by Yufeng Wu (2019) <doi:10.1093/bioinformatics/btz676>. 'scistreer' provides an 'R' interface and improves speed via 'Rcpp' and 'RcppParallel', making the method applicable to massive single-cell datasets (>10,000 cells).
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2025-10-09 |
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perl-cgi
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public |
A generic file fetching mechanism.
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2025-10-09 |
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gencove
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public |
Gencove is a high-throughput, cost-effective platform for genome sequencing and analysis. This command-line interface can be used to easily access the Gencove API.
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2025-10-09 |
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flumutdb
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public |
Utility module for FluMut database.
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2025-10-09 |
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perl-specio
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public |
Type constraints and coercions for Perl
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2025-10-09 |
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rust-gtars
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public |
Performance-critical tools to manipulate, analyze, and process genomic interval data.
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2025-10-09 |
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epimetheus-py
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public |
CLI tool for fast lookup in pileup for motif methylation.
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2025-10-09 |
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xclone
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public |
Inference of clonal Copy Number Alterations in single cells.
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2025-10-09 |
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iseq
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public |
iSeq is a Bash script that allows you to download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
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2025-10-09 |
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gbdraw
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public |
A genome diagram generator for microbes and organelles.
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2025-10-09 |
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ibridges
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public |
Package for accessing data and metadata on iRods servers.
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2025-10-09 |
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dxpy
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public |
DNAnexus Platform API bindings for Python
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2025-10-09 |
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centrosome
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public |
An open source image processing library. Dependency for CellProfiler
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2025-10-09 |
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bifidoannotator
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public |
Fine-grained annotation of bifidobacterial enzymes involved in human-milk glycan (HMG) utilization
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2025-10-09 |
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mgnify-pipelines-toolkit
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public |
Collection of scripts and tools for MGnify pipelines.
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2025-10-09 |
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impg
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public |
impg: implicit pangenome graphs.
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2025-10-09 |
