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Search results for r rna seq
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rna-seq
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88 search results found
Nichenetr
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416
NicheNet: predict active ligand-target links between interacting cells
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
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
Rnaseq Workflow
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133
A repository for setting up a RNAseq workflow
Tximport
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128
Transcript quantification import for modular pipelines
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.
Clustifyr
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93
Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
Sartools
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87
Statistical Analysis of RNA-Seq Tools
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.
Single Cell Training
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63
SIB course on single cell transcriptomics by mostly using the Seurat pipeline
Irap
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58
integrated RNA-seq Analysis Pipeline
Learnbioconductor
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56
Training material for introductory R / Bioconductor courses
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
Tomicsvis
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50
Transcriptomics Visualization R package.
Cellnet
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48
CellNet: network biology applied to stem cell engineering
Derfinder
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42
Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
Recount
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40
R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
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
Dgca
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38
Differential Gene Correlation Analysis
Tcc Gui
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37
📊 Graphical User Interface for TCC package
Tdm
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36
R package for normalizing RNA-seq data to make them comparable to microarray data.
Datest
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34
Compare different differential abundance and expression methods
Grein
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30
GREIN : GEO RNA-seq Experiments Interactive Navigator
Wiggleplotr
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28
A small R package to make sequencing read coverage plots in R.
Ideal
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28
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
Combat Seq
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28
Batch effect adjustment based on negative binomial regression for RNA sequencing count data
Deepstats
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27
deepStats: a stastitical toolbox for deeptools and genomic signals
Omicselector
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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.
Vigen
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24
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
M3drop
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24
Rna Seq Tutorial For Gene Differential Expression Analysis
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24
This tutorial is created for educational purpose
Recount3
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24
Explore and download data from the recount3 project
Bitfam
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23
BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.
Beyondcell
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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.
Fraser
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22
FRASER - Find RAre Splicing Events in RNA-seq
Alpine
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22
Modeling and correcting fragment sequence bias for RNA-seq
Popsicler
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22
popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.
Splicejam
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21
Sashimi plots for RNA-seq data using detected transcripts
Degreport
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21
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
Rna Seq Snakemake
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20
Snakemake based pipeline for RNA-Seq analysis
Microscope
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17
ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps
Cd4 Csaw
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15
Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
Splatter Paper
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15
Data and analysis for the Splatter paper
Dropclust
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15
Version 2.1.0 released
Parser
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15
parseR: Pipeline for rna-seq analysis in R
Dseqr
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15
single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.
Ularcirc
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14
An R-shiny app that provides backsplice and canonical splicing analysis for both circular RNA (circRNA) and parental transcripts
Eagle
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14
An R package for detecting Gene-by-Environment (GxE) interaction effects on the transcriptome using Allele Specific Expression quantified from RNA-seq
Bgeedb_r
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13
Source code of the R packge BgeeDB to use data from the Bgee database
Gseabenchmarker
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13
Reproducible GSEA Benchmarking
Scmut
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13
Topconfects
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13
TOP results by CONfident efFECT Sizes.
Rnaseq
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13
RNA-seq, QC and differential analysis pipeline
Npdr
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12
NPDR: Nearest-neighbor Projected-Distance Regression with the generalized linear model
Atacr
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12
Analysing Capture Seq Count Data
Recount Website
⭐
12
Code for the Recount project
Circompara
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12
🔬 A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data
Ebaii
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12
Supports de cours de l'Ecole de Bioinformatique Aviesan - IFB - Inserm "Initiation au traitement des données de génomique obtenues par séquençage à haut débit"
Spotclean
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11
R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
Sci Plex
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11
repository containing analysis scripts and auxiliary files
Archive Ruvseq
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11
Archived version of RUVSeq
Hcir
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11
R package for RNA-seq workflows at HCI
Hermes
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10
Preprocessing, analyzing, and reporting of RNA-seq data
Regionreport
⭐
9
Generate HTML report for a set of genomic regions or DESeq2/edgeR results
Ancetran
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9
AnceTran2.0: R package for transcriptome evolution analysis based on RNA-seq expression data or ChIP-seq TF-binding data
Pyreqtl
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9
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.
Arpir
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9
Automatic RNA-Seq Pipelines with Interactive Report
Sequenza
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8
Workflow for Sequenza, cellularity and ploidy
Rrmsanalyzer
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8
A set of easy-to-use functions to analyze end read count data of RiboMethSeq (RNA 2'Ome)
Splicelauncher
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8
RNAseq pipeline for alternative splicing junctions
Mtd
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8
MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
Deseq2shiny
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8
a web-based R shiny application that wraps DESeq2 R package
Hcadata
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7
Access data from the Human Cell Atlas project, directly via R/Bioconductor
Trendcatcher
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7
TrendCatcher is an open source R-package that allows users to systematically analyze and visualize time course data. Please cite "Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19" by Xinge Wang et al published in JCI Insight (2022) - https://insight.jci.org/articles/view/157255
Sere
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7
SERE: single-parameter quality control and sample comparison for RNA-Seq
Arseq
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7
An Automated RNASeq Analysis Pipeline (Differential expression to gene enrichment)
Bp4rnaseq
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7
An automated pipe for reproducible RNA-seq analysis with the minimal efforts from researchers. You only need to provide the taxa name and the accession code of RNA-seq samples deposited in the National Center for Biotechnology Information (NCBI). After a cup of tea or longer, you will get formatted gene expression data as gene count, transcript count and TPM values, etc.
Scmagic
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6
Accurately annotating scRNA-seq data using two rounds of reference-based classification
Signals
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6
Single Cell Genomes with Allele Specificity
Ppcseq
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6
Probabilistic outlier identification for bulk RNA sequencing data
Knowseq
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6
KnowSeq R package
Tag Seq
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6
3’ Tag RNA-seq pipeline (Work in progress)
Dturtle
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6
Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:
As_analysis
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5
A complete Snakemake pipeline for detecting allele specific expression
Muren
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5
MUREN: a Robust and Multi-reference Approach of RNA-seq Transcript Normalization
Recount Contributions
⭐
5
Contribute your human Illumina RNA-seq data to recount2
Scdva
⭐
5
An R shiny based tool used for single cell RNA-seq data visualization and analysis.
Celltalkdb
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5
A manually curated database of literature-supported ligand-receptor interactions in human and mouse
Baerhunter
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5
Jaffelab
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5
R package with commonly used functions by the Jaffe lab
Digitaldlsorter
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5
digitalDLSorteR: An R package to deconvolute bulk RNA-Seq using scRNA-Seq data
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