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UCSF
- San Francisco
- www.semiquant.com
- https://orcid.org/0000-0002-7893-8416
Stars
Friends don't let friends make certain types of data visualization - What are they and why are they bad.
nf-core / scflow
Forked from combiz/nf-core-scflowPlease consider using/contributing to https://github.com/nf-core/scdownstream
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
helper script to analyze nanopore run of umi data
Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
Newest iteration of PurpleDrop. Reimplemented in kicad5
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
Reconstruction of transmission trees using genomic data
Plotting tools for nanopore methylation data
SigMa is a probabilistic model for the sequential dependencies of mutation signatures
GAEseq: A Graph Auto-Encoder for Haplotype Assembly and Viral Quasispecies Reconstruction
Visualise interstrain recombination from environmental samples.
Segmented HAPlotype Estimation and Imputation Tool
phasing and Allele Specific Expression from RNA-seq
A python package storing different tools for different NGS operations
QuantTB is a SNP based method to identify and quantify individual strains present in tuberculosis whole genome sequencing datasets.
List of software packages for multi-omics analysis
vtreat is a data frame processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner. Distributed under choice of GPL-2 or GPL-3 license.
Variant Ensemble Filter, an ensemble based filter for VCF files.