#
bioinformatics-pipeline
Here are 399 public repositories matching this topic...
A language and runtime for distributed, incremental data processing in the cloud
language
golang
aws
data-science
runtime
bioinformatics-pipeline
scientific-computing
cloud-computing
analysis-pipeline
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Updated
Aug 11, 2021 - Go
Analysis Pipeline for Single Cell ATAC-seq
machine-learning-algorithms
sequencing
epigenetics
bioinformatics-pipeline
single-cell-analysis
single-cell-atac-seq
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Updated
Mar 3, 2021 - R
Rapid large-scale prokaryote pan genome analysis
bioinformatics
research
genomics
pathogen
sequencing
next-generation-sequencing
bioinformatics-pipeline
global-health
infectious-diseases
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Updated
Sep 26, 2020 - Perl
saketkc
commented
Feb 26, 2021
Google colab now supports Python 3.7, which is the minimum requirement for pysradb. All the notebooks in notebooks/ need to be transitioned to Python 3.7 (they stopped working from pysradb 1.0 onwards)
Finds SNP sites from a multi-FASTA alignment file
bioinformatics
research
genomics
pathogen
sequencing
next-generation-sequencing
bioinformatics-pipeline
global-health
infectious-diseases
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Updated
Dec 16, 2020 - C
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
bioinformatics
research
genomics
pathogen
sequencing
next-generation-sequencing
bioinformatics-pipeline
global-health
infectious-diseases
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Updated
Oct 13, 2020 - Java
ATAC-seq and DNase-seq processing pipeline
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Updated
Sep 25, 2019 - Python
A tool to circularize genome assemblies
bioinformatics
research
genomics
pathogen
sequencing
next-generation-sequencing
bioinformatics-pipeline
global-health
infectious-diseases
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Updated
Apr 13, 2021 - Python
unode
commented
Feb 28, 2019
When working with very large SAM files it is often convenient to remove sequence and quality information to reduce storage and improve I/O.
Following from this it would be convenient to have a stripSeqQual function that replaces the two fields with *.
Antimicrobial Resistance Identification By Assembly
bioinformatics
research
genomics
pathogen
sequencing
next-generation-sequencing
bioinformatics-pipeline
global-health
infectious-diseases
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Updated
Jul 9, 2021 - Python
GCP Essentials for Bioinformatics Researchers
cloud
bioinformatics
genomics
gcp
bioinformatics-pipeline
bioinformatics-analysis
bioinformatics-researchers
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Updated
Aug 10, 2021 - Jupyter Notebook
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
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Updated
Jun 1, 2021 - Jupyter Notebook
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
epigenetics
bioinformatics-pipeline
dna-methylation
differential-methylation
functional-genomics
nome-seq
nome-seq-data
calling-dmrs
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Updated
Jul 2, 2021 - Python
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
bioinformatics
research
genomics
pathogen
sequencing
next-generation-sequencing
bioinformatics-pipeline
global-health
infectious-diseases
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Updated
Jul 27, 2021 - C
A modular annotation tool for genomic variants
javascript
python
bioinformatics
genomics
python3
bioinformatics-pipeline
annotation-tool
variant-annotations
variant-annotation
variant-analysis
genomic-data-analysis
bioinformatics-tool
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Updated
Aug 31, 2021 - JavaScript
AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
python
bam-files
clustering
graphical-interface
pagerank
bioinformatics-pipeline
alternative-splicing
command-line-tool
splicing-quantification
network-analysis
pathway-analysis
rna-seq-data
scrna-seq-data
cell-cycle
cell-type-classification
splicing-visualization
fastq-anaysis
single-cell-splicing
marker-gene-analysis
louvain-community-detection
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Updated
Jul 25, 2021 - Python
Cluster single cells and analyze cell clade relationships with colorful visualizations.
visualization
bioinformatics-pipeline
single-cell
bioinformatics-algorithms
single-cell-rna-seq
single-cell-analysis
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Updated
Aug 27, 2021 - Haskell
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
bioinformatics
rna-seq
snakemake
pipeline
reproducible-research
ngs
bioinformatics-pipeline
chip-seq
atac-seq
workflows
fastq
sra
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Updated
Sep 1, 2021 - Python
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
bioinformatics
snakemake
virus
ngs
sequencing
conda
bioinformatics-pipeline
biohackeu20
biohackcovid20
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Updated
Aug 31, 2021 - Python
Infectious Disease Sequencing Platform
science
bioinformatics
research
genomics
biology
sequencing
computational-biology
next-generation-sequencing
bioinformatics-pipeline
global-health
virology
infectious-diseases
metagenomic
idseq
idseq-web
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Updated
Sep 1, 2021 - Ruby
A bioinformatics pipeline to analyze mtDNA from NGS data
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Updated
Feb 25, 2021 - Python
A collection of reusable WDL tasks. Category:Other
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Updated
Aug 26, 2021 - wdl
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
bioinformatics
bioinformatics-pipeline
phylogenetics
orthology
homology
ncbi-sra
gene-sequence-retrieval
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Updated
Apr 2, 2021 - Python
A pipeline and a framework for NGS analysis (RNA-Seq and soon Chip-Seq)
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Updated
Sep 1, 2021 - Java
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
python
snakemake
intellij
eap
moment
bioinformatics-pipeline
pycharm
gear
bioinformatics-tool
intellij-plugins
eap-updates
platform-ides
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Updated
Aug 27, 2021 - Python
Improve the quality of a denovo assembly by scaffolding and gap filling
bioinformatics
research
genomics
pathogen
sequencing
next-generation-sequencing
bioinformatics-pipeline
global-health
infectious-diseases
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Updated
Jan 4, 2021 - Perl
A handy pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
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Updated
Aug 26, 2021 - Python
See the main fork of this repository here >>>
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Updated
May 12, 2021 - Nextflow
de novo virus assembler of Illumina paired reads
bioinformatics
research
genomics
pathogen
sequencing
next-generation-sequencing
bioinformatics-pipeline
global-health
infectious-diseases
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Updated
May 17, 2021 - Python
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As reported by @jonalv , it can be confusing what is happening when if the globber pattern does not catch any files.
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