AngieHinrichs

lineage-designation-B

RSV-B lineage definitions and proposals

nextclade_to_maple

Converts nextclade TSV output to MAPLE input

nhoodStats

science project: find gene clusters for various window sizes, compute avg neighborhood correlation & p-values

samtabix

This is a merge of AngieHinrichs/samtools (lh3/samtools patched to allow alternate network lib and not check EOF) and tabix-0.2.6 downloaded from samtools.sourceforge.net. I replaced samtools' bgzf.[ch] with tabix's because tabix's seemed more recent. Had to modify some samtools files to work with updated bgzf.h.

SARS-CoV-2_Sequencing

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

ncov-ingest

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

USHER_DEMO

kent

UCSC Genome Browser source tree. Stable branch: "beta".

usher

Ultrafast Sample Placement on Existing Trees

AngieHinrichs/lineage-designation-B

RSV-B lineage definitions and proposals

AngieHinrichs/nextclade_to_maple

Converts nextclade TSV output to MAPLE input

AngieHinrichs/nhoodStats

science project: find gene clusters for various window sizes, compute avg neighborhood correlation & p-values

AngieHinrichs/samtabix

This is a merge of AngieHinrichs/samtools (lh3/samtools patched to allow alternate network lib and not check EOF) and tabix-0.2.6 downloaded from samtools.sourceforge.net. I replaced samtools' bgzf.[ch] with tabix's because tabix's seemed more recent. Had to modify some samtools files to work with updated bgzf.h.

AngieHinrichs/samtools

This is Angie Hinrichs' fork of Heng Li's lh3/samtools, which describes itself as "*NOT* the official repository of samtools"; therefore this is even less official. I have applied a patch that adds a wrapper mode to knetfile, so that alternate network libraries (such as UCSC Genome Browser's kent/src/) can be hooked in.

AngieHinrichs/augur

Pipeline components for real-time phylodynamic analysis

AngieHinrichs/bioconda-recipes

Conda recipes for the bioconda channel.

AngieHinrichs/constellations

AngieHinrichs/COVID-19-Lab-Specific-Bias-Filter

We developed a tool to systematically flag COVID-19 genomes for variants resulting from possible lab specific biases. The program requires a concurrent nextstrain VCF file, nextstrain parsimony file and nextstrain metadata file as input. It outputs two tsv files: one with each flagged snp and the respective reasoning underlying the flag, and another providing more detailed information on each flagged lab.

AngieHinrichs/G-NEST

The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin. Example data files are in the separate repository G-NEST_examples:

AngieHinrichs/h9_seg8_clade

AngieHinrichs/hgvslib

hgvslib provides functions to parse and compare the equivalency of variant strings described according to Human Genome Variation Society (HGVS) syntax.

AngieHinrichs/lineage-designation-A

RSV-A lineage definitions and proposals

AngieHinrichs/lineages-website

AngieHinrichs/mpxv-lineage-designation

Updates and details of monkeypox virus lineages designations

AngieHinrichs/ncov-ingest

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

AngieHinrichs/pango-designation

Repository for suggesting new lineages that should be added to the current scheme

AngieHinrichs/pangoLEARN

Store of the trained model for pangolin to access.

AngieHinrichs/pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

AngieHinrichs/pangolin-assignment

The latest lineage assignments from pangolin.

AngieHinrichs/pangolin-data

Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments

AngieHinrichs/SARS-CoV-2_Sequencing

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

AngieHinrichs/sarscov2lineages

AngieHinrichs/sarscov2phylo

Global phylogenies of SARS-CoV-2 sequences

AngieHinrichs/strain_phylogenetics

AngieHinrichs/taxonium

A tool for exploring very large trees in the browser

AngieHinrichs/usher

Ultrafast Sample Placement on Existing Trees

AngieHinrichs/USHER_DEMO

AngieHinrichs/usher_wiki

docs holder for usher wiki