Projects in Awesome Lists tagged with ngs-analysis

https://github.com/open2c/bioframe

Genomic interval operations on Pandas DataFrames

bioinformatics dataframes genomic-intervals genomic-ranges genomics ngs-analysis numpy pandas python spatial-join

Last synced: 20 Dec 2024

https://github.com/JhuangLab/BioInstaller

A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform

bioinformatics-analysis installer installer-script ngs-analysis

Last synced: 04 Dec 2024

https://github.com/sib-swiss/ngs-variants-training

GitHub for the SIB courses NGS - Genome variant analysis

course gatk ngs ngs-analysis teaching training tutorial variant-calling

Last synced: 28 Nov 2024

https://github.com/sib-swiss/ngs-introduction-training

SIB course that introduces analysis of NGS data

course ngs-analysis teaching training tutorial

Last synced: 28 Nov 2024

https://github.com/afrendeiro/toolkit

A toolkit for NGS analysis with Python

atac-seq bioinformatics chip-seq looper ngs ngs-analysis project-management pypiper rna-seq

Last synced: 15 Nov 2024

https://github.com/soedinglab/bammmotif2

Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.

bioinformatics chip-seq motif-analysis motif-discovery ngs-analysis

Last synced: 11 Nov 2024

https://github.com/wckdouglas/sequencing_tools

A python package storing different tools for different NGS operations

bam-files fastq ngs ngs-analysis rna rna-seq-analysis

Last synced: 08 Dec 2024

https://github.com/czheluo/mbsa

Multple methods for BSA Pipeline

bsa bsr fine-mapping ngs-analysis qtl-analyses rnaseq stats

Last synced: 18 Nov 2024

https://github.com/cchrysostomou/seqtables

Tools for analyzing NGS sequence data and aligned protein sequences

aligned-sequences dna ngs-analysis ngstools pandas plotly protein

Last synced: 12 Oct 2024

https://github.com/slowkow/saturation

:sponge: Estimate sequencing saturation for GEX, VDJ, and ADT data from the 10x Genomics platform.

10xgenomics bioinformatics gene-expression ngs-analysis vdj

Last synced: 03 Dec 2024

https://github.com/lumc/hutspot

Multisample DNAseq variant calling pipeline for use in diagnostics

biocontainers bioinformatics ngs-analysis ngs-pipeline singularity snakemake snakemake-workflows

Last synced: 02 Dec 2024

https://github.com/mskcc/facets2n

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

allele-specific copy-number-variation ngs ngs-analysis

Last synced: 12 Nov 2024

https://github.com/lumc/vtools

Various tools operating over VCF files. Uses cyvcf2 and cython under the hood for speed

bioinformatics bioinformatics-tool ngs-analysis vcf

Last synced: 02 Dec 2024

https://github.com/lumc/gnomad-merge

Snakemake pipeline to merge gnomAD VCF files

ngs ngs-analysis snakemake snakemake-workflow

Last synced: 02 Dec 2024

https://github.com/imamachi-n/docker-bioconda2

bioinformatics biology docker ngs-analysis

Last synced: 19 Nov 2024

https://github.com/meeranhussain/population_genomic_analysis

A repository for efficient population genomic analysis using Snakemake workflow.

genome-analysis ngs ngs-analysis population population-genomics rprogramming snakemake-workflow variant-calling whole

Last synced: 10 Nov 2024

https://github.com/wckdouglas/liftover_bam

bam-files dna-seq ngs-analysis rna-seq

Last synced: 08 Dec 2024

https://github.com/quantori/crisprseqsim

CRISPRSeqSim is a tool that simulates results of CRISPR/cas editing fragments target sequencing.

amplicon-sequencing bioinformatics crispr-analysis illumina ngs-analysis python read-simulation

Last synced: 10 Nov 2024

https://github.com/pritampanda15/ngs-workflows

Next-generation Sequencing workflows

nextflow nextflow-pipelines ngs ngs-analysis ngs-pipeline python3 r snakemake workflow workflow-automation

Last synced: 28 Nov 2024

https://github.com/dohlee/hiv1-rloop

💻 Analysis codes and bioinformatic pipelines for paper "HIV-1-induced host genomic R-loops dictate HIV-1 integration site selection"

ngs-analysis pipeline reproducible-research rna-seq

Last synced: 11 Nov 2024

https://github.com/leooojr/reprohackathon

A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.

apptainer bash bowtie cli cutadapt deseq2 fastqc featurecounts google-cloud-platform hpc nextflow ngs-analysis ngs-pipeline r samtools shell sratoolkit ubuntu

Last synced: 20 Nov 2024

https://github.com/llrs/ngs

Making some comparisons of NGS data

alcoholic-liver-disease ngs-analysis

Last synced: 22 Dec 2024