limfuxing / ruvIIInbLinks
This package removes unwanted variation from raw sequencing count data using Negative Binomial and/or Zero Inflated Negative Binomial model. Thus far, the package has been applied to remove unwanted variation from single-cell RNA-seq and shotgun metagenomics data. The package takes raw sequencing count as input and thus in principle can be appli…
☆18Updated last year
Alternatives and similar repositories for ruvIIInb
Users that are interested in ruvIIInb are comparing it to the libraries listed below
Sorting:
- An R package to analyze single-cell V(D)J data☆28Updated last year
- Scripts to install as a Bioconda package for making workflows☆17Updated last year
- Bead-based single-cell atac processing☆33Updated 3 years ago
- satuRn is a highly performant and scalable method for performing differential transcript usage analyses.☆22Updated 2 years ago
- scover☆24Updated last year
- Snakemake pipeline for benchmarking cell-type deconvolution methods and deconvolving real bulk RNA-seq data with the use of scRNA-seq dat…☆15Updated 6 months ago
- Inferring gene co-expression networks from single cell gene expression data☆28Updated 3 years ago
- Calculation of distance metrics for matrices☆26Updated 6 years ago
- R package for Flexible dot plots☆29Updated 3 years ago
- Allele-Specific Expression by Single-Cell RNA Sequencing☆29Updated 5 years ago
- ADTnorm normalizes the cell surface protein measurement of CITE-seq data, facilitating across batches and across studies data integration…☆24Updated 3 months ago
- Lightweight Iterative Gene set Enrichment in R☆57Updated last year
- Comprehensive pipeline for donor demultiplexing in single cell☆24Updated last week
- Single-cell RNA Processing Software☆11Updated 4 months ago
- Tool to parse fasterq/fastq dump outputs for SRA scRNAseq data☆17Updated last year
- Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq☆13Updated last year
- A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations☆35Updated 3 years ago
- SCASA: Single cell transcript quantification tool☆22Updated last year
- An R for fast and flexible DNA methylation analysis☆34Updated 3 weeks ago
- Exon-Intron Split Analysis (EISA) in R☆16Updated last month
- A single cell sequencing read simulator.☆33Updated last year
- Isoform co-usage networks from single-cell RNA-seq data☆16Updated last year
- ☆41Updated 3 years ago
- ☆29Updated 2 years ago
- Human brain, >200,000 nuclei☆24Updated 4 years ago
- Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes☆44Updated 4 years ago
- Trans-association between HLA and TCR-CDR3☆18Updated 2 years ago
- Clone identification from single-cell data☆61Updated 2 years ago
- Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.☆57Updated last year
- Snakefile-based process to turn 1.4 million ocular cells into a unified meta-atlas☆26Updated last year