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Search results for rna seq

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IRIS: Isoform peptides from RNA splicing for Immunotherapy target Screening

Open_pipelines ⭐ 17

Pipelines for NGS data preprocessing by the Bock lab and friends

Fast in-silico normalization algorithm for NGS data

Rna Seq Pop ⭐ 17

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Rpanglaodb ⭐ 17

An R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database into a Seurat object.

Pipernaseq ⭐ 16

A comprehensive pipeline for RNAseq data analysis

Cd4 Csaw ⭐ 15

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

Pyflow Rnaseq ⭐ 15

RNAseq pipeline based on snakemake

Pipelines in genomics

Dropclust ⭐ 15

Version 2.1.0 released

Dynamical systems methods for RNA velocity analysis

Splatter Paper ⭐ 15

Data and analysis for the Splatter paper

parseR: Pipeline for rna-seq analysis in R

Subread_to_dexseq ⭐ 15

A way to use FeatureCounts output for DEXSeq

Msisensor Rna ⭐ 15

MSIsensor-RNA: Microsatellite instability detection using RNA sequencing data

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.

Rnaseqmut ⭐ 14

RNA-Seq Mutation Detection

Gdc Rnaseq Tool ⭐ 14

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

An R package for detecting Gene-by-Environment (GxE) interaction effects on the transcriptome using Allele Specific Expression quantified from RNA-seq

Uncurl_python ⭐ 14

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

GCEN: an easy-to-use toolkit for Gene Co-Expression Network analysis and lncRNAs annotation

Ngs_data_analysis_course ⭐ 14

Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)

Ularcirc ⭐ 14

An R-shiny app that provides backsplice and canonical splicing analysis for both circular RNA (circRNA) and parental transcripts

Rnaseqreadsimulator ⭐ 14

RNASeqReadSimulator is a simple tool to generate simulated single-end or paired-end RNA-Seq reads.

Pavfinder ⭐ 14

🔍 Post Assembly Variants Finder

Transindel ⭐ 13

Indel caller for DNA-seq or RNA-seq

RNA-seq, QC and differential analysis 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

Lr Splitpipe ⭐ 13

Demultiplexing and debarcoding tool designed for LR-Split-seq data.

Flexible omics pipeline

Topconfects ⭐ 13

TOP results by CONfident efFECT Sizes.

A toolkit for NGS analysis with Python

Gseabenchmarker ⭐ 13

Reproducible GSEA Benchmarking

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

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

Workflows ⭐ 12

CWL based Bioinformatics Workflows

Chimerate ⭐ 12

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

Workshop Ngsintro ⭐ 12

Workshop • Intro to Bioinformatics using NGS data • 5 days

Recount Website ⭐ 12

Code for the Recount project

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

Seq Pipeline ⭐ 12

Workspace for data science projects and NGS pipelines. Contains RStudio, Jupyter Notebook, VSCode and file manager. Can connect to Tailscale network to bypass firewalls.

NPDR: Nearest-neighbor Projected-Distance Regression with the generalized linear model

Rna Seq In The Cloud ⭐ 12

An Easy to Use Analysis System for All Human Public bulk RNAseq Data!

Rcount: simple and flexible RNA-Seq read counting

Circompara ⭐ 12

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

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.

Analysing Capture Seq Count Data

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

Phenotypexpression ⭐ 11

Subclassification of disease states based on the intersection of literature and expression

Archive Ruvseq ⭐ 11

Archived version of RUVSeq

Sci Plex ⭐ 11

repository containing analysis scripts and auxiliary files

Rna Combine ⭐ 11

RNA-seq data comprehensive data analysis toolbox

Xpresspipe ⭐ 11

An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data

Oncofuse ⭐ 11

Predicting oncogenic potential of gene fusions

Isonclust2 ⭐ 11

A tool for de novo clustering of long transcriptomic reads

R package for RNA-seq workflows at HCI

Rnaseq Introduction Training ⭐ 11

Webpage of the "Introduction to RNA-Seq: From quality control to pathway analysis - streamed" SIB course.

Spotclean ⭐ 11

R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data

Rpkm_rnaseq_count ⭐ 11

RPKM for RNASeq counts

Couplednmf ⭐ 11

Coupled clustering of single cell genomic data

A Unified RNA Sequencing Model (URSM) for joint analysis of single cell and bulk RNA-seq data.

Modulome Workflow ⭐ 10

Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA

Dl Based Tumor Classification ⭐ 10

Deep Learning Based Tumor Type Classification Using Gene Expression Data

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

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

Tostadas ⭐ 10

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

Preprocessing, analyzing, and reporting of RNA-seq 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.

Piperiboseq ⭐ 10

A comprehensive pipeline for Ribo-seq data analysis

Oyster_river_protocol ⭐ 10

Official Repository of the Oyster River Protocol for Transcriptome Assembly

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.

Geneexpressionaging ⭐ 10

Gene expression viewer template

Tag Based_rnaseq ⭐ 10

Cost-efficient genome-wide gene expression profiling

Visualization and management of denovo transcriptomes

AnceTran2.0: R package for transcriptome evolution analysis based on RNA-seq expression data or ChIP-seq TF-binding data

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.

Automatic RNA-Seq Pipelines with Interactive Report

Brainseq_phase2 ⭐ 9

BrainSeq Phase II project lead by LIBD for the BrainSeq Consortium

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

Regionreport ⭐ 9

Generate HTML report for a set of genomic regions or DESeq2/edgeR results

Rnaseq Pipeline ⭐ 9

RNASeq-Pipeline for Quantification and Enrichment Analysis

Star Seqr ⭐ 9

RNA Fusion Detection and Quantification

Trackcluster ⭐ 9

An analysis pipeline for Nanopore direct-RNA sequencing

Single-Cell Spatial Explorer

Workflow for Sequenza, cellularity and ploidy

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

exRNA Biomarker Discovery for Liquid Biopsy

DEbPeak - Analyze and integrate multi-omics to unravel the regulation of gene expression.

Deseq2shiny ⭐ 8

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

Rnaseq Cb321 ⭐ 8

A tool to extract and annotate genes from raw RNA-seq reads.

Fatecompass ⭐ 8

Splicelauncher ⭐ 8

RNAseq pipeline for alternative splicing junctions

Rrmsanalyzer ⭐ 8

A set of easy-to-use functions to analyze end read count data of RiboMethSeq (RNA 2'Ome)

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

A comprehensive quality-control and quantification RNA-seq pipeline

Related Searches

R Rna Seq (194)

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Pipeline Rna Seq (111)

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