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109 search results found

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Deeptools ⭐ 644

Tools to process and analyze deep sequencing data.

Pydeseq2 ⭐ 470

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Single Cell Pseudotime ⭐ 367

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

Youtubetutorials ⭐ 180

Bioc Refcard ⭐ 170

Bioconductor cheat sheet

Rnaseq Workflow ⭐ 133

A repository for setting up a RNAseq workflow

Seq2science ⭐ 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.

Rnaseqc ⭐ 132

Fast, efficient RNA-Seq metrics for quality control and process optimization

Single cell analysis in the browser

Rnalysis ⭐ 114

RNA sequencing analysis software

Geoparse ⭐ 98

Python library to access Gene Expression Omnibus Database (GEO)

Isoquant ⭐ 98

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Biojupies ⭐ 94

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

Dolphinnext ⭐ 92

A graphical user interface for distributed data processing of high throughput genomics

Callings Nf ⭐ 76

GATK RNA-Seq Variant Calling in Nextflow

Startapp ⭐ 71

The START App: R Shiny Transcriptome Analysis Resource Tool

Single Cell Training ⭐ 63

SIB course on single cell transcriptomics by mostly using the Seurat pipeline

Snakefiles ⭐ 58

🐍 Snakefiles for common RNA-seq data analysis workflows.

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

𝐠𝐠𝐯𝐨𝐥𝐜 effortlessly translates differential expression datasets and RNAseq data into informative volcano plots. Highlight genes of interest with unprecedented ease. With just a single line of code, visualize complex datasets, gaining deeper insights and simplifying data representation

Tomicsvis ⭐ 50

Transcriptomics Visualization R package.

Ngi Rnaseq ⭐ 49

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

Agfusion ⭐ 46

Python package to annotate and visualize gene fusions.

A fully automated gene annotator from RNA-Seq expression data

Cell2cell ⭐ 44

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

Metasra Pipeline ⭐ 42

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

Deep Learning based cell composition analysis with Scaden.

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

📊 Graphical User Interface for TCC package

Genome Annotation Pipeline ⭐ 36

Genome annotation pipeline

Spatialtranscriptomics ⭐ 34

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Picardmetrics ⭐ 34

🚦 Run Picard on BAM files and collate 90 metrics into one file.

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Reademption ⭐ 31

A pipeline for the computational evaluation of RNA-Seq data

Workshop Rnaseq ⭐ 30

Workshop • Analysis of RNA-seq data

Transabyss ⭐ 30

de novo assembly of RNA-seq data using ABySS

Metaomgraph ⭐ 30

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

A python package and a set of shell commands to handle GTF files

Next-Gen Sequencing tools from the Horvath Lab

Rnaseq_titration_results ⭐ 29

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

Volcano3d ⭐ 28

An R package to plot interactive three-way differential expression analysis

Biotoolbox ⭐ 27

Tools for querying and analysis of genomic data

Soapdenovo Trans ⭐ 27

SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.

Smallrnaseq ⭐ 26

small rna-seq analysis package

Omicselector ⭐ 26

OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.

Zavolan-Lab Automated RNA-Seq Pipeline

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)

Pipeliner ⭐ 25

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

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

Mudskipper ⭐ 25

A tool for projecting genomic alignments to transcriptomic coordinates

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

ASAP : Automated Single-cell Analysis Pipeline

Beyondcell ⭐ 23

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments.

Project Manager for NGS data analysis

Rna Seq Snakemake ⭐ 20

Snakemake based pipeline for RNA-Seq analysis

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

Pigx_rnaseq ⭐ 19

Pipeline for RNAseq

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Slamdunk ⭐ 18

Streamlining SLAM-seq analysis with ultra-high sensitivity

Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.

Open_pipelines ⭐ 17

Pipelines for NGS data preprocessing by the Bock lab and friends

Pipernaseq ⭐ 16

A comprehensive pipeline for RNAseq data analysis

Splatter Paper ⭐ 15

Data and analysis for the Splatter paper

parseR: Pipeline for rna-seq analysis in R

Uncurl_python ⭐ 14

UNCURL is a tool for single cell RNA-seq data analysis.

Gdc Rnaseq Tool ⭐ 14

Tool to download/merge RNASeq data from the GDC Portal in matrices identified by TCGA barcode

Pavfinder ⭐ 14

🔍 Post Assembly Variants Finder

Gene Oracle ⭐ 13

Feature extraction algorithm for genomic data

Bgeedb_r ⭐ 13

Source code of the R packge BgeeDB to use data from the Bgee database

A toolkit for NGS analysis with Python

Flexible omics pipeline

Community effort to evaluate computational methods for the detection and quantification of poly(A) sites and estimating their differential usage across RNA-seq samples

Circompara ⭐ 12

🔬 A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data

Chimerate ⭐ 12

A pipeline to detect chimeric transcripts derived from genes and transposable elements.

Workflows ⭐ 12

CWL based Bioinformatics Workflows

Analysing Capture Seq Count Data

Workshop Ngsintro ⭐ 12

Workshop • Intro to Bioinformatics using NGS data • 5 days

Supports de cours de l'Ecole de Bioinformatique Aviesan - IFB - Inserm "Initiation au traitement des données de génomique obtenues par séquençage à haut débit"

Efp Seq_browser ⭐ 12

An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level.

Rna Combine ⭐ 11

RNA-seq data comprehensive data analysis toolbox

Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.

Oncofuse ⭐ 11

Predicting oncogenic potential of gene fusions

Dl Based Tumor Classification ⭐ 10

Deep Learning Based Tumor Type Classification Using Gene Expression Data

Bioinformatics ⭐ 10

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.

Enrichment_analysis ⭐ 10

A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.

Tostadas ⭐ 10

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

NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization

Mapping-free software for fishing relevant reads in an RNA-Seq sample

Piperiboseq ⭐ 10

A comprehensive pipeline for Ribo-seq data analysis

A toolset for handling sequencing data with unique molecular identifiers (UMIs)

A collection of Python modules equivalent to R ReQTL Toolkit aims to identify the association between expressed SNVs with their gene expression using RNA-sequencing data.

Trackcluster ⭐ 9

An analysis pipeline for Nanopore direct-RNA sequencing

Deseq2shiny ⭐ 8

a web-based R shiny application that wraps DESeq2 R package

MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

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