Teaching

This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

Categories > Science > Genomics

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Science > Genomics

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Project Name	Stars	Repos Using This	Packages Using This	Most Recent Commit	Total Releases	Latest Release	Open Issues	License	Language
Deepvariant	2,978			7 months ago			8	bsd-3-clause	Python
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Gatk	1,576		2	3 months ago	46	March 16, 2023	1,299	other	Java
Official code repository for GATK versions 4 and up
Galaxy	1,211	2	23	5 months ago	30	December 08, 2023	2,169	other	Python
Data intensive science for everyone.
Getting Started With Genomics Tools And Resources	991			5 months ago			1		Shell
Unix, R and python tools for genomics and data science
Adam	966	20	17	5 months ago	14	December 16, 2020	35	apache-2.0	Scala
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Sarek	299			5 months ago			180	mit	Nextflow
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Fgbio	292			5 months ago	16	May 16, 2023	110	mit	Scala
Tools for working with genomic and high throughput sequencing data.
Truvari	284			3 months ago	23	August 07, 2023		mit	Python
Structural variant toolkit for VCFs
Htsjdk	271	170	87	6 months ago	78	October 13, 2023	303		Java
A Java API for high-throughput sequencing data (HTS) formats.
Sequenceserver	259	1		5 months ago	68	October 05, 2023	91	agpl-3.0	JavaScript
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

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Deepvariant ⭐ 2,978

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

most recent commit 7 months ago

Gatk ⭐ 1,576

Official code repository for GATK versions 4 and up

dependent packages 2total releases 46most recent commit 3 months ago

Galaxy ⭐ 1,211

Data intensive science for everyone.

dependent packages 23total releases 30most recent commit 5 months ago

Getting Started With Genomics Tools And Resources ⭐ 991

Unix, R and python tools for genomics and data science

most recent commit 5 months ago

Adam ⭐ 966

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

dependent packages 17total releases 14most recent commit 5 months ago

Sarek ⭐ 299

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

most recent commit 5 months ago

Fgbio ⭐ 292

Tools for working with genomic and high throughput sequencing data.

total releases 16most recent commit 5 months ago

Truvari ⭐ 284

Structural variant toolkit for VCFs

total releases 23most recent commit 3 months ago

Htsjdk ⭐ 271

A Java API for high-throughput sequencing data (HTS) formats.

dependent packages 87total releases 78most recent commit 6 months ago

Sequenceserver ⭐ 259

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

total releases 68most recent commit 5 months ago

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Teaching vs Gatk

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Teaching vs Getting Started With Genomics Tools And Resources

Teaching vs Sequenceserver

Popular Genomics Projects

Biopython ⭐ 3,918

Official git repository for Biopython (originally converted from CVS)

dependent packages 1,373total releases 58latest release February 13, 2023most recent commit 5 months ago

Seurat ⭐ 2,025

R toolkit for single cell genomics

dependent packages 2total releases 16latest release November 13, 2022most recent commit 5 months ago

Deeplearning Biology ⭐ 1,846

A list of deep learning implementations in biology

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Minimap2 ⭐ 1,613

A versatile pairwise aligner for genomic and spliced nucleotide sequences

dependent packages 32total releases 27latest release December 26, 2021most recent commit 5 months ago

Bwa ⭐ 1,282

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

total releases 1latest release March 03, 2021most recent commit a year ago

Popular Sequencing Projects

Fastp ⭐ 1,602

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.

total releases 1latest release December 15, 2021most recent commit 8 months ago

Samtools ⭐ 1,496

Tools (written in C using htslib) for manipulating next-generation sequencing data

most recent commit 5 months ago

Ncov ⭐ 1,348

Nextstrain build for novel coronavirus SARS-CoV-2

most recent commit 5 months ago

Picard ⭐ 914

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

dependent packages 12total releases 176latest release November 14, 2023most recent commit 5 months ago

Rnaseq ⭐ 718

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

most recent commit 5 months ago

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