TimoLassmann/tagdust

A tool to extract mappable reads from various library preparation protocols.

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TimBlokker/RNA_Sequencing

In total there are 3 jupyter notebooks together with 3 html files for ease of access in this repository. (1) Master notebook & FastQC and Mapping of reads using star and subsequent feature count (this notebook), (2) the DESeq2 analysis in R for the statistical analysis, (3) Functional analysis using arbitrary (GProfiler, iRegulon) and "leading edge" (Gorilla, GSEA) cut-offs. The dataset was taken from here: https://www.ncbi.nlm.nih.gov/sra/SRX8335650 and is accompanying the publication by Carmona-Rivera et al. 2020 https://insight.jci.org/articles/view/139388.

Language: Jupyter Notebook - Size: 3.05 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

praneet1988/CSBB-Shiny

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

Language: R - Size: 2.85 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 29 - Forks: 13

chgibb/unMappedCIGARFragments

Extract unmapped read fragments from a sequence alignment map by evaluating it's concise idiosyncratic gapped alignment reports (CIGARs)

Language: TypeScript - Size: 577 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

ANSES-Ploufragan/DUGMO

Detection of unknown genetically modified organisms

Language: Python - Size: 208 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

Holin-Chen/coronavirus-CpG-genetic-analysis

A genetic sequence analysis on calculating the GC contents and CpG deficiencies on multiple coronaviruses (SAR-CoV, SAR-CoV-2, MERS-CoV and 2 two bat derived SARS-like coronaviruses) to see which coronavirus has the most potentially effective mechanism to escape the anti-virus activities on human bodies.

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ARYrt/VirusMAPPER

This program is able to align reads to a database with genomes of reference and support single or paired-end reads from Illumina sequencing technology in FASTQ format (or fastq.gz)

Language: Python - Size: 7.07 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

rbr7/bioinformatics_courses

A repository for maintaining assignments and projects, from courses done in bioinformatics and CB.

Language: Jupyter Notebook - Size: 10.4 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

BenbowLab/Benin-NGS

Example files for Benin NGS capacity building project

Language: HTML - Size: 1.36 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

rodriguez-salarichs/FastC

FastC aims to provide a simple way to do some quality control checks on treated sequence data. It is similar to FastQC allowing a comparative study between raw and processed data.

Language: C++ - Size: 25.1 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

ncbi/pm4ngs

Project Manager for NGS data analysis

Language: Python - Size: 14 MB - Last synced at: 12 months ago - Pushed at: over 2 years ago - Stars: 25 - Forks: 10

FSUgenomics/SRSFN

SRSF framework for nucleosome positioning analysis

Language: PostScript - Size: 329 KB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

FSUgenomics/SRSFseq

SRSF shape analysis framework for sequencing data

Language: R - Size: 3.94 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 2

DanielRCA/MTDNA-CR

Raw code to get polymorphisms from samples analysed by using the PowerSeq® CRM Nested System kit (Promega Corporation)

Language: Shell - Size: 38.1 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

AbdelrahmanYahia/GUAP_toolkit

Genomics unit analysis pipelines toolkit: a collection of NGS workflows writtin in python3 and snakemake

Language: Python - Size: 1.83 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

GeneMAP-Research/projects

Research projects conducted at the GeneMAP Research Center

Size: 58.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

rptashkin/facets2n

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

Language: R - Size: 240 MB - Last synced at: 26 days ago - Pushed at: almost 3 years ago - Stars: 6 - Forks: 4

ARUP-NGS/cobalt

Cobalt is a tool to detect copy-number variants from next generation sequencing (NGS) data

Language: Python - Size: 30.3 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 1

TC-Hewitt/MuTrigo

pipeline for mutant gene candidate discovery

Language: Python - Size: 81.1 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

zhanghao-njmu/NGSmodule

A flexible, automation and pragmatic workflow tool to process the NGS data.

Language: R - Size: 1.98 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 2

jordanlab/STing

Ultrafast sequence typing and gene detection from NGS raw reads

Language: C++ - Size: 25.9 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 18 - Forks: 2

EstherOlabisi/Bioinformatics-work

Several bioinformatics projects: sequence alignment, machine learning, GUI development, etc.

Language: R - Size: 13.2 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

mccoy-lab/LD-PGTA

Linkage disequlibrium-informed PGT-A (LD-PGTA). A package for detecting genotypic signatures of aneuploidy from extremely low-coverage sequence data.

Language: Python - Size: 10.5 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 10 - Forks: 0

LUMC/vtools

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

Language: Python - Size: 204 KB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

quantori/CRISPRSeqSim

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

Language: Python - Size: 24.4 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

cma2015/deepEA

deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data

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IdoBar/A_rabiei_WGS_analysis

Whole-Genome-Sequencing analysis pipeline of Ascochyta rabiei isolates

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AbdelrahmanYahia/wes_gatk

Whole exome sequencing snakemake workflow based on GATK best practice

Language: Jupyter Notebook - Size: 23.1 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

rmoffitt/GeneSetMatch

A tool for deep statistical analyses and informative visualizations of complex -omic data

Language: HTML - Size: 189 MB - Last synced at: 18 days ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

Pg-Pi3Gey/ms-chikv-deg

main Repository for my Master's Thesis work

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MobiDL/tasks

A collection of tasks wrapped in WDL

Language: wdl - Size: 695 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 1

esharathgoud/Data-Analysis

linked with Bioinformatics analysis

Language: Shell - Size: 5.86 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

katerinakazantseva/sysbio_RNASeq

Size: 6.03 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

NCBI-Hackathons/ScrubSV

A QC pipeline for SVs calls based on coverage and SNP calls

Language: R - Size: 189 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 0

BU-ISCIII/plasmidID

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

Language: Shell - Size: 91.8 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 35 - Forks: 8

molevol-ub/BacterialDuplicates

Identification of putative duplicated genes among bacterial genomes

Language: Perl - Size: 2.22 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 1

skchronicles/pyrkit

A tool to archive and co-locate NGS data with project-level, sample-level, and analysis-specific metadata.

Language: Python - Size: 4.57 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 3

manojbhosale/ngsUtils

Useful NGS utilities for everyday use in the form of stand-alone tool.

Language: Java - Size: 5.4 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

OrangePomeranian/Bachelor_thesis

The performance of individual CNV detection software and state-of-the-art sequencing. All analyses were performed using the Python and R programming languages.

Language: Python - Size: 36.1 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

Candlelight-XYJ/Bioinformatics-Project

生物信息学项目实践仓库🏆🥇

Language: Shell - Size: 22.7 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 22 - Forks: 10

odb9402/CNNPeaks

The ChIP-Seq peak calling algorithm using convolution neural networks

Language: Python - Size: 16.2 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 13 - Forks: 3

RIVM-bioinformatics/AminoExtract

AminoExtract is a tool for translating and extracting amino acid sequences from nucleotide-sequences based on a GFF input

Language: Python - Size: 115 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 1 - Forks: 0

DeplanckeLab/Meireles-Filho_Litovchenko2019

Source code to support the paper: “Extensive tissue-specific expression variation and novel regulators underlying circadian behavior”

Language: R - Size: 786 KB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

zhuochenbioinfo/RiceReseqCNV

Mining CNV based on rice Nipponbare genome using resequencing data.

Language: Perl - Size: 21.8 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

guillaume-gricourt/HmnTrimmer

Fast-polyvalent trimmer used for several applications of next-generation sequencing

Language: HTML - Size: 11.9 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

JKlesmith/PACT

Protein Analysis and Classifier Toolkit

Language: Python - Size: 1.72 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 0

Wangyiquan95/NA_EPI

We apply combinatorial mutagenesis and next-generation sequencing to characterize the local fitness landscape in an antigenic region of NA in six different human H3N2 strains that were isolated around 10 years apart. This pipeline is used to analyze data and plotting.

Language: Jupyter Notebook - Size: 40.3 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 2

niekwit/RNA-Seq

RNA-Seq pipeline

Language: Python - Size: 71.3 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

SouthGreenPlatform/TOGGLE

Toolbox for generic NGS analyses - A framework to quickly build pipelines and to perform large-scale NGS analysis

Language: Perl - Size: 168 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 18 - Forks: 5

RIVM-bioinformatics/TrueConsense

TrueConsense is a consensus caller for viral-targets that create biologically correct consensus sequences. TrueConsense keeps track of open reading frames, compensates for common sequencing or alignment artefacts, and is able to generate consensus sequences on multiple coverage-thresholds at the same time

Language: Python - Size: 1.02 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 0

wckdouglas/sequencing_tools

A python package storing different tools for different NGS operations

Language: HTML - Size: 4.83 MB - Last synced at: 29 days ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 0

bioinfoUQAM/mirLibSpark

microRNA validation using Spark framework

Language: Java - Size: 443 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0

beatrizmclm/2.NGS_QC_analysis_and_alignment_in_R

Quality control and processing of NGS data

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isinaltinkaya/adv_binf_2021_week1

Teaching material used in the "Advanced Bioinformatics for Next-Generation Sequencing" class, University of Copenhagen, 2021

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Edert/R-scripts

Useful R-scripts by edert

Language: R - Size: 26.4 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

wckdouglas/liftover_bam

Language: Python - Size: 55.7 KB - Last synced at: 29 days ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

dduv-ddit/highlander

GUI coupled to a local database that centralize all NGS variant data and annotations, and to provide powerful filtering tools that are easily accessible to the biologist.

Language: Java - Size: 124 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

he-hai/breseq_script

Script for using breseq at MPI-TM & MPI-MP

Language: Shell - Size: 6.84 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

dandyrilla/hsptrim

FASTQ read trimming by the highest scoring path algorithm

Language: Python - Size: 1.95 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

arminms/amstools

Common bioinformatic tools in C/C++

Language: C++ - Size: 43 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

V-Z/RAD-Seq-scripts

Set of scripts to process RAD-Seq HTS data on computing grids like MetaCentrum.

Language: Shell - Size: 5.14 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

jlchen5/sequencing-read-depth-calculate

The repository is used to calculate the NGS data sequencing read depth.

Language: Shell - Size: 8.79 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

lzy604/ChIP-seq

ChIP-seq

Language: R - Size: 298 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

yaan-jang/leri

Leri Analytics delivers bioinformatics services for and solutions to both the academic labs and industries.

Size: 285 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

lzy604/RNA-seq

RNA-seq analysis

Language: R - Size: 50.8 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

koushik20/BRCA_RNA-Seq_Analysis

RNA-seq analysis workflow using DESeq2

Language: R - Size: 1.94 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

propan2one/OshV-1-molepidemio

Code of the article that describes the molecular epidemiology analyses of OsHV-1 virus by whole genome sequencing approaches in French shellfish growing areas.

Language: Shell - Size: 7.17 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1

babinyurii/apobec

NGS data analysis scripts for HBV elimination research group

Language: Python - Size: 1.45 MB - Last synced at: 3 days ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 1

Hattyoriiiiiii/single-cell-scripts

scripts for scRNA-Seq/scATAC-Seq

Language: R - Size: 1000 Bytes - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

Hattyoriiiiiii/ngs-scripts

Language: Shell - Size: 27.3 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

SinomeM/CNVgears

An R package to integrate and analyze CNV calling results from multiple methods in a uniformed and standardized manner

Language: R - Size: 10.8 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 2

cchrysostomou/seqtables

Tools for analyzing NGS sequence data and aligned protein sequences

Language: Python - Size: 92.4 MB - Last synced at: 5 days ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 2

garcia-nacho/FHI_SC2_Pipeline_Nanopore

Bioinformatic pipeline for SARS-CoV-2 sequence analysis

Language: Shell - Size: 15.5 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

garcia-nacho/FHI_SC2_Pipeline_Illumina

Bioinformatic pipeline for SARS-CoV-2 sequence analysis

Language: R - Size: 14.1 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

mkarlik93/MetaPlastHunter

Language: Python - Size: 966 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0

jennylsmith/fusBreakpoint

R package for Sequence Search in BAM files using R Bioconductor

Language: R - Size: 99.6 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

biocompute-objects/bco-public-website Fork of nanxstats/bco-public-website

A Hugo-based deployment of biocomputeobject.org

Language: HTML - Size: 16.8 MB - Last synced at: about 6 hours ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

hebamuh68/BOOKS

Exercises and Implementation

Language: Python - Size: 2.22 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

ficusrobusta/Protein-Binding-Affinity-Next-Generation-Sequencing-Data-Analysis

Data science project, analysing NGS data from a binding study,

Language: Jupyter Notebook - Size: 1000 KB - Last synced at: 8 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

PankratzLab/SuperNovo

DeNovo Mutation Identification and Validation

Language: Java - Size: 24.4 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

LUMC/hutspot

Multisample DNAseq variant calling pipeline for use in diagnostics

Language: Python - Size: 5.98 MB - Last synced at: 23 days ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 2

bissessk/RNA-seq-Analysis-of-Control-and-NRDE2-depleted-Breast-Cancer-Cells

Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.

Language: Shell - Size: 418 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

CEGRcode/cegr-yep-qcviz

Galaxy YEP Qc & Viz workflow invocation scripts and input datasets

Language: HTML - Size: 39.6 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

angelovangel/nextflow-bcl-shiny

a shiny frontend for the nextflow-bcl pipeline

Language: R - Size: 58.6 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

marialitovchenko/BRB-seq_pipeline

Development of the user-friendly interface for the BRB-seq

Language: JavaScript - Size: 4.31 MB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

ANGSD-wrapper/angsd-wrapper

Utilities for analyzing next generation sequencing data.

Language: Shell - Size: 13.4 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 13 - Forks: 4

appliedbinf/URDO-SMOREd

Sequence Matching fOr REpiratory Diseases, SMORE'D, is a command-line sequence classification tool tailored to meet the needs of the Undiagnosed Respiratory Disease Outbreak (URDO) branch at CDC. SMORE'D is a k-mer based classification tool capable of rapidly classifying read sequences generated by multi-pathogen detection platforms.

Language: Python - Size: 24.5 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 1

emlec/SSV-Coverage Fork of mathieubolteau/SSV-Coverage

Coverage graph creator from BAM files (included in the SSV-Conta package)

Language: Python - Size: 200 KB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

vpeddu/CMV-NIPT

Hunting for CMV and HHV-6 in cfDNA sequence

Language: R - Size: 4.06 MB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 1

praneet1988/Computational-Suite-For-Bioinformaticians-and-Biologists

Computational Suite For Bioinformaticians and Biologists (CSBB) provides 18 modules focused on analytical tasks like performing upper-quantile normalization, interactive visualization and next generation sequencing pipelines. CSBB now also has capability to process public data. Providing User with End to End pipeline experience

Language: Perl - Size: 3.86 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1

LUMC/gnomad-merge

Snakemake pipeline to merge gnomAD VCF files

Language: Python - Size: 59.6 KB - Last synced at: about 1 month ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

AmyL19/DriverFinder

Size: 21.7 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

Imamachi-n/Docker-Bioconda2

Language: Python - Size: 1.59 MB - Last synced at: about 1 month ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

llrs/NGS

Making some comparisons of NGS data

Language: HTML - Size: 23.4 MB - Last synced at: 18 days ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0

snewhouse/exotic-dna-ngs

WIP & POC: Count Viral and other non-human genome signatures in Human NGS data

Language: Shell - Size: 114 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 0

amelieff/NGS_handson_2016

NGSハンズオン講習会2016年 NGS解析基礎、RNA-seq、Reseq、ChIP-seq資料

Size: 7.78 MB - Last synced at: almost 2 years ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 1