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Search results for bioinformatics snakemake
bioinformatics
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snakemake
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48 search results found
Metagem
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155
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Seq2science
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132
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.
Snakefmt
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131
The uncompromising Snakemake code formatter
Multiprime
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123
multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))
V Pipe
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119
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
Smk Simple Slurm
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80
A simple Snakemake profile for Slurm without --cluster-config
Tibanna
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68
Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
Panoptes
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59
Monitor computational workflows in real time
Snakefiles
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58
🐍 Snakefiles for common RNA-seq data analysis workflows.
Sv Callers
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52
Snakemake-based workflow for detecting structural variants in genomic data
Dentist
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44
Close assembly gaps using long-reads at high accuracy.
Pipelines.jl
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39
A lightweight and powerful Julia package for computational pipelines and workflows.
Lsf
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29
Snakemake profile for running jobs on an LSF cluster
Zarp
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26
Zavolan-Lab Automated RNA-Seq Pipeline
Atacseq_pipeline
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25
Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.
Phylociraptor
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23
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
Iliad
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21
ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications
Rna Seq Snakemake
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20
Snakemake based pipeline for RNA-Seq analysis
Assemblycomparator2
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20
🦠📇 Compare prokaryotic genomic assemblies
Pigx_rnaseq
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19
Pipeline for RNAseq
Kgwasflow
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19
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
Mosaicatcher Pipeline
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19
Integrated workflow for SV calling from single-cell Strand-seq data
Vesselexpress
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17
🔬🖥 Automated Blood Vasculature Analysis of 3D Light-Sheet Image Volumes
Daylily
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15
A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.
Snakemake Novice Bioinformatics
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14
Introduction to Snakemake for Bioinformatics
Snakemake Wrappers
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14
🐍 Snakemake wrappers for bioinformatics.
Qadabra
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13
Snakemake workflow for comparison of differential abundance ranks
Ymp
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13
Flexible omics pipeline
Transflow
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12
A snakemake workflow for WGS-based tuberculosis transmission analysis
Ngs Pipeline
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12
Pipeline for Somatic Variant Calling with WES and WGS data
Enrichment_analysis
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10
A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.
Pigx_bsseq
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10
bisulfite sequencing pipeline from fastq to methylation reports
Riboraptor
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9
Tool for ribo-seq analysis
Triti Map
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9
A Snakemake-based pipeline for gene mapping in Triticeae.
Hribo
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8
We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, and integrates them with additional computed features. This facilitates both the rapid discovery of ORFs and their prioritization for functional charact
Project Diploid Assembly
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8
Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data
Snakemake_rnaseq
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8
A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)
Multiple_sclerosis_proj
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8
Data analysis platform/structure, machine learning/AI project for multiple sclerosis
Lepwrap
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7
A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.
Mapp
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7
🗺️ MAPP is a computational method which enables identification of binding motifs for RNA-binding proteins that shape pre-mRNA processing under specific conditions.
Spritz
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6
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
Dea_seurat
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6
A Snakemake workflow for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
Uorf Tools
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6
uORF-Tools are a workflow and a collection of tools for the analysis of 'Upstream Open Reading Frames' (short uORFs)
Paqr2
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5
Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository.
Metagenomics
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5
Snakemake workflow for functional analysis of metagenomic WGS read data.
Genome_tracks
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5
A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.
Xebec
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5
Snakemake pipeline for microbiome diversity effect size benchmarking
Sars2seq
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5
SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.
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1-48 of 48 search results
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