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Search results for rna seq
rna-seq
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386 search results found
Rnaseq
⭐
718
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Salmon
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661
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Deeptools
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644
Tools to process and analyze deep sequencing data.
Rna Seq Analysis
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614
RNAseq analysis notes from Ming Tang
Kallisto
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601
Near-optimal RNA-Seq quantification
Single Cell Best Practices
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544
https://www.sc-best-practices.org
Pydeseq2
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470
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Nichenetr
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416
NicheNet: predict active ligand-target links between interacting cells
Single Cell Pseudotime
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367
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
Snakepipes
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359
Customizable workflows based on snakemake and python for the analysis of NGS data
Scrna Tools
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295
Table of software for the analysis of single-cell RNA-seq data.
Mixcr
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291
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
Training Material
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284
A collection of Galaxy-related training material
Rna Seq Star Deseq2
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282
RNA-seq workflow using STAR and DESeq2
Sleuth
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266
Differential analysis of RNA-Seq
Zumis
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232
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
Youtubetutorials
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180
Sccatch
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171
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
Bioc Refcard
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170
Bioconductor cheat sheet
Arriba
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165
Fast and accurate gene fusion detection from RNA-Seq data
Dittoseq
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153
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
Bambu
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150
Reference-guided transcript discovery and quantification for long read RNA-Seq data
Armor
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146
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
Sequana
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136
Sequana: a set of Snakemake NGS pipelines
Rnaseq Workflow
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133
A repository for setting up a RNAseq workflow
Rnaseqc
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132
Fast, efficient RNA-Seq metrics for quality control and process optimization
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.
Kana
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131
Single cell analysis in the browser
Tximport
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128
Transcript quantification import for modular pipelines
Xpore
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122
Identification of differential RNA modifications from nanopore direct RNA sequencing
Rnafusion
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120
RNA-seq analysis pipeline for detection gene-fusions
Scrnaseq
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119
A single-cell RNAseq pipeline for 10X genomics data
Fusioncatcher
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117
Finder of Somatic Fusion Genes in RNA-seq data
Alevin Fry
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115
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
Drop
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114
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
Rnalysis
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114
RNA sequencing analysis software
Omicsplayground
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112
Visual self-service analytics platform for big omics data.
Powsimr
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102
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
Geoparse
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98
Python library to access Gene Expression Omnibus Database (GEO)
Isoquant
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98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Whippet.jl
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96
Lightweight and Fast; RNA-seq quantification at the event-level
Pipeline Transcriptome De
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95
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
Biojupies
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94
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
Clustifyr
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93
Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
Dolphinnext
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92
A graphical user interface for distributed data processing of high throughput genomics
Sartools
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87
Statistical Analysis of RNA-Seq Tools
Tophat
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83
Spliced read mapper for RNA-Seq
Spark
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81
Publication quality NGS track plotting
Sg Nex Data
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80
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
Callings Nf
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76
GATK RNA-Seq Variant Calling in Nextflow
Tpmcalculator
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74
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
Pychopper
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74
A tool to identify, orient, trim and rescue full length cDNA reads
Zika Rnaseq Pipeline
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73
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
Scrnaseqpipeline
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73
Startrac
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71
STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)
Scnym
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71
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
Startapp
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71
The START App: R Shiny Transcriptome Analysis Resource Tool
Epic
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68
Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
Diffexpr
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67
Porting DESeq2 into python via rpy2
Rna Bloom
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66
🌺 reference-free transcriptome assembly for short and long reads
Single Cell Training
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63
SIB course on single cell transcriptomics by mostly using the Seurat pipeline
Rna Seq Kallisto Sleuth
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63
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
Trinity_ctat
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63
Lorean
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62
Long Reads Annotation pipeline
Feelnc
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61
FEELnc : FlExible Extraction of LncRNA
Covid 19 Rna Seq Datasets
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61
A repository for sharing information on available COVID-19 RNA-Seq datasets
Shinyngs
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60
Shiny apps for NGS etc based on reusable components created using Shiny modules
Rnaseq Nf
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59
A proof of concept of RNAseq pipeline
Snakefiles
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58
🐍 Snakefiles for common RNA-seq data analysis workflows.
Irap
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58
integrated RNA-seq Analysis Pipeline
Threedrnaseq
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58
A pipeline for differential expression and differential alternative splicing analysis
Learnbioconductor
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56
Training material for introductory R / Bioconductor courses
Degust
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55
An interactive web-tool for RNA-seq analysis
Kallistobustools
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55
kallisto | bustools workflow for pre-processing single-cell RNA-seq data
Cello
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53
CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology
Rattle
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51
Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
Intro To Rnaseq Hpc Salmon Flipped
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51
Introduction to bulk RNA-seq
Jaffa
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51
JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
Poreplex
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51
A versatile sequenced read processor for nanopore direct RNA sequencing
Scflow
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50
Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.
Ggvolc
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50
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
Eoulsan
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50
A pipeline and a framework for NGS analysis (RNA-Seq and soon Chip-Seq)
Tomicsvis
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50
Transcriptomics Visualization R package.
Ngi Rnaseq
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49
Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
Cellnet
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48
CellNet: network biology applied to stem cell engineering
Agfusion
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46
Python package to annotate and visualize gene fusions.
Pipeliner
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44
An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
Cell2cell
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44
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
Finder
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44
A fully automated gene annotator from RNA-Seq expression data
Terminus
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43
Derfinder
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42
Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
Metasra Pipeline
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42
MetaSRA: normalized sample-specific metadata for the Sequence Read Archive
Dapars
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41
DaPars(Dynamic analysis of Alternative PolyAdenylation from RNA-seq)
Clustering_on_transcript_compatibility_counts
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40
Clustering cells from single cell RNA seq assays
Cellxgene Gateway
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40
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
Outrider
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40
OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
Protocols 4pub
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40
Multi-omics analysis protocols by Lyu.
Sprint
⭐
40
SNP-free RNA editing Identification Toolkit
Scaden
⭐
40
Deep Learning based cell composition analysis with Scaden.
Recount
⭐
40
R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
Related Searches
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