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Search results for pipeline conda

65 search results found

Deeplearningproject ⭐ 4,043

An in-depth machine learning tutorial introducing readers to a whole machine learning pipeline from scratch.

Nextflow ⭐ 2,447

A DSL for data-driven computational pipelines

Elyra ⭐ 1,721

Elyra extends JupyterLab with an AI centric approach.

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Atac Seq Pipeline ⭐ 290

ENCODE ATAC-seq pipeline

Bactopia ⭐ 281

A flexible pipeline for complete analysis of bacterial genomes

Chip Seq Pipeline2 ⭐ 188

ENCODE ChIP-seq pipeline

Maestro ⭐ 181

Single-cell Transcriptome and Regulome Analysis Pipeline

Sunbeam ⭐ 157

A robust, extensible metagenomics pipeline

Comparative Annotation Toolkit ⭐ 137

Atac_dnase_pipelines ⭐ 135

ATAC-seq and DNase-seq processing pipeline

Dropseqpipe ⭐ 134

A SingleCell RNASeq pre-processing snakemake workflow

SkyPy: A package for modelling the Universe.

Plant Seg ⭐ 81

A tool for cell instance aware segmentation in densely packed 3D volumetric images

Rescript ⭐ 74

REference Sequence annotation and CuRatIon Pipeline

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.

Nanoclust ⭐ 59

NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads

Low-level data processing pipeline software for the Cherenkov Telescope Array

Automatic DNA methylation detection from nanopore tools and their consensus model

Ncov Tools ⭐ 44

Small collection of tools for performing quality control on coronavirus sequencing data and genomes

Pipelines Nextflow ⭐ 41

A set of workflows written in Nextflow for Genome Annotation.

Strain Resolution ON Graphs

Mtbseq_source ⭐ 32

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Mlf Core ⭐ 31

CPU and GPU deterministic and therefore fully reproducible machine learning pipelines using MLflow.

Scib Pipeline ⭐ 30

Snakemake pipeline that works with the scIB package to benchmark data integration methods.

Wochenende ⭐ 30

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

Mpraflow ⭐ 27

A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data

Persvade ⭐ 27

perSVade: personalized Structural Variation detection

Provenance ⭐ 26

Provenance and caching library for python functions, built for creating lightweight machine learning pipelines

Pore C Snakemake ⭐ 25

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Software for Quantifying Interspersed Repeat Expression

Scasat is a single cell ATAC-seq preprocessing and analysis pipeline

Single-cell Transcriptome and Regulome Analysis Pipeline.

Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.

Seqcap_processor ⭐ 20

Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics

SPANDx - Comparative genomics for next-generation haploid sequence data

Mageckflute ⭐ 20

Integrative analysis pipeline for pooled CRISPR functional genetic screens

snakemake pipeline for Hi-C post-processing

Kgwasflow ⭐ 19

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Bactpipe ⭐ 17

BACTpipe: An assembly and annotation pipeline for bacterial genomics

Comprehensive resistance detection from WGS data

Research pipeline for exploring clinically relevant genomic variants

Proteoformer ⭐ 14

Integration ribosome profiling - mass spectrometry

🧛 Deep generative models for TCR sequences 🧛

Clickbait Workshop ⭐ 13

Pydata 2017 workshop: build a clickbait detector with python

Riboflow ⭐ 12

Pipeline for Ribosome Profiling Data

Metagenomic Analysis

The Vertebrate Genomes Project Mitogenome Assembly Pipeline

A pipeline for bioinformatics analysis of bacterial genomes

Nature_methods_multicut_pipeline ⭐ 11

Hamronization_workflow ⭐ 11

Harmonization of AMR predictor tool outputs

Strainsifter ⭐ 10

A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).

Cascabel ⭐ 10

Automated pipeline for amplicon sequence analysis

Instance_stixels ⭐ 10

Implementation of the Instance Stixel pipeline. Paper:

Dropseqrunner ⭐ 10

Lightweight pipeline for processing droplet-based single-cell RNA-seq data

Tostadas ⭐ 10

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Cam_server ⭐ 9

Camera server to convert EPICS enabled cameras into bsread cameras.

Databricks Connect Pyspark ⭐ 9

A guide of how to build good Data Pipelines with Databricks Connect using best practices

BMO - a tool for predicting TF binding from ATAC-seq data

Snakemake_rnaseq ⭐ 8

A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)

Calibration for HST/WFC3, HST/ACS, and HST/STIS

Automated QIIME 2 Workflow wrapped in Luigi Framework currently in early development

Building A Robust Machine Learning Pipeline ⭐ 7

Diagnosisextraction_ml ⭐ 6

Pipeline for building Machine Learning Classifiers for the diagnosis of EHR text-data. We used this pipeline for our study, published here: https://doi.org/10.2196/23930.

Tagseq Qiime2 Snakemake ⭐ 6

Pipeline to run qiime2 with snakemake

Biodendro ⭐ 6

A package to cluster and visualise MS/MS spectral data

Nxf Fastqc ⭐ 5

A simple fastp-MultiQC nextflow pipeline

RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department

Nal_rna_seq_annotation_pipeline ⭐ 5

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