Elvers(formerly eelpond) an automated RNA-Seq workflow system
Stars: ✭ 22 (-56.86%)
ScipipeRobust, flexible and resource-efficient pipelines using Go and the commandline
Stars: ✭ 826 (+1519.61%)
VdjvizA lightweight immune repertoire browser
Stars: ✭ 21 (-58.82%)
PyensemblrestA wrapper for the EnsEMBL REST API
Stars: ✭ 25 (-50.98%)
KhmerIn-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Stars: ✭ 640 (+1154.9%)
Sv CallersSnakemake-based workflow for detecting structural variants in WGS data
Stars: ✭ 28 (-45.1%)
CookiecutterDEPRECIATED! Please use nf-core/tools instead
Stars: ✭ 18 (-64.71%)
Locuszoom StandaloneCreate regional association plots from GWAS or meta-analysis
Stars: ✭ 35 (-31.37%)
HailScalable genomic data analysis.
Stars: ✭ 706 (+1284.31%)
ScanpySingle-Cell Analysis in Python. Scales to >1M cells.
Stars: ✭ 858 (+1582.35%)
Metacachememory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Stars: ✭ 26 (-49.02%)
Cs Video CoursesList of Computer Science courses with video lectures.
Stars: ✭ 27,209 (+53250.98%)
ProtrComprehensive toolkit for generating various numerical features of protein sequences
Stars: ✭ 30 (-41.18%)
MigmapHTS-compatible wrapper for IgBlast V-(D)-J mapping tool
Stars: ✭ 38 (-25.49%)
Helmsmanhighly-efficient & lightweight mutation signature matrix aggregation
Stars: ✭ 19 (-62.75%)
PybedgraphA Python package for fast operations on 1-dimensional genomic signal tracks
Stars: ✭ 17 (-66.67%)
VerifybamidVerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
Stars: ✭ 44 (-13.73%)
SeqtkToolkit for processing sequences in FASTA/Q formats
Stars: ✭ 799 (+1466.67%)
CromwellScientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Stars: ✭ 655 (+1184.31%)
GenevalidatorGeneValidator: Identify problems with predicted genes
Stars: ✭ 34 (-33.33%)
NonpareilEstimate metagenomic coverage and sequence diversity
Stars: ✭ 26 (-49.02%)
16gtSimultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Stars: ✭ 26 (-49.02%)
HtslibC library for high-throughput sequencing data formats
Stars: ✭ 529 (+937.25%)
FastpAn ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Stars: ✭ 966 (+1794.12%)
Tiledb VcfEfficient variant-call data storage and retrieval library using the TileDB storage library.
Stars: ✭ 26 (-49.02%)
GatkOfficial code repository for GATK versions 4 and up
Stars: ✭ 1,002 (+1864.71%)
EmaFast & accurate alignment of barcoded short-reads
Stars: ✭ 24 (-52.94%)
Cytometry Clustering ComparisonR scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data
Stars: ✭ 30 (-41.18%)
Fusiondirect.jl(No maintenance) Detect gene fusion directly from raw fastq files
Stars: ✭ 23 (-54.9%)
LigerLightweight Iterative Gene set Enrichment in R
Stars: ✭ 44 (-13.73%)
JampJAMP - Just Another Metabarcoding Pipeline
Stars: ✭ 19 (-62.75%)
RasusaRandomly subsample sequencing reads to a specified coverage
Stars: ✭ 28 (-45.1%)
Nsga Iian implementation of NSGA-II in java
Stars: ✭ 18 (-64.71%)
UtaUniversal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
Stars: ✭ 38 (-25.49%)
Splatter PaperData and analysis for the Splatter paper
Stars: ✭ 17 (-66.67%)
Sevenbridges RSeven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R
Stars: ✭ 27 (-47.06%)
ManormA robust model for quantitative comparison of ChIP-Seq data sets.
Stars: ✭ 16 (-68.63%)
DramDistilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Stars: ✭ 47 (-7.84%)
GalaxyData intensive science for everyone.
Stars: ✭ 812 (+1492.16%)
Minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequences
Stars: ✭ 912 (+1688.24%)
MultiqcAggregate results from bioinformatics analyses across many samples into a single report.
Stars: ✭ 708 (+1288.24%)
EtrfExact Tandem Repeat Finder (not a TRF replacement)
Stars: ✭ 35 (-31.37%)
React Plotly.jsA plotly.js React component from Plotly 📈
Stars: ✭ 701 (+1274.51%)
Uncurl pythonUNCURL is a tool for single cell RNA-seq data analysis.
Stars: ✭ 13 (-74.51%)
NucleusPython and C++ code for reading and writing genomics data.
Stars: ✭ 657 (+1188.24%)
Awesome VdjTools and databases for analyzing HLA and VDJ genes.
Stars: ✭ 43 (-15.69%)
SeqkitA cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
Stars: ✭ 607 (+1090.2%)
ScispacyA full spaCy pipeline and models for scientific/biomedical documents.
Stars: ✭ 855 (+1576.47%)
CsvtkA cross-platform, efficient and practical CSV/TSV toolkit in Golang
Stars: ✭ 566 (+1009.8%)
BwaBurrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Stars: ✭ 970 (+1801.96%)
Taxadb🐣 locally query the ncbi taxonomy
Stars: ✭ 26 (-49.02%)
YacrdYet Another Chimeric Read Detector
Stars: ✭ 49 (-3.92%)
SnsAnalysis pipelines for sequencing data
Stars: ✭ 43 (-15.69%)
SinglecellhaystackFinding surprising needles (=genes) in haystacks (=single cell transcriptome data).
Stars: ✭ 41 (-19.61%)
Metasra PipelineMetaSRA: normalized sample-specific metadata for the Sequence Read Archive
Stars: ✭ 33 (-35.29%)
PretzelJavascript full-stack framework for Big Data visualisation and analysis
Stars: ✭ 26 (-49.02%)