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Search results for rna seq

rna-seq x
386 search results found
Nextgenseq_pipeline ⭐ 8
Exome/Capture/RNASeq Pipeline Implementation using snakemake
Bgee_pipeline ⭐ 8
Source code of the Bgee pipeline used to build the Bgee database
Fluentgenomics ⭐ 7
plyranges and tximeta case study
Discotoolkit_py ⭐ 7
DISCO by Scientist for Scientist for You
Metafusion ⭐ 7
Sirvsuite ⭐ 7
SIRVsuite is a command line tool to QC an RNA-Seq workflow using Lexogen's SIRV spike-in controls.
Trendcatcher ⭐ 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
Braincode ⭐ 7
Script and pipeline for BRAINcode project
Varus ⭐ 7
RNA-Seq sampling
Sere ⭐ 7
SERE: single-parameter quality control and sample comparison for RNA-Seq
Arseq ⭐ 7
An Automated RNASeq Analysis Pipeline (Differential expression to gene enrichment)
Hu_molcell_2017 ⭐ 7
"Dissecting cell-type composition and activity-dependent transcriptional state in mammalian brains by massively parallel single-nucleus RNA-Seq"
Bp4rnaseq ⭐ 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.
Dualrnaseq ⭐ 7
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
Scmmd ⭐ 7
Maximum mean discrepancy comparisons for single cell profiling experiments
Nease ⭐ 7
A network-based approach for exon set enrichment
Aerobio ⭐ 7
Extensible full DAG streaming computation server with services and jobs for RNA-Seq, Tn-Seq, WG-Seq and Term-Seq.
Hcadata ⭐ 7
Access data from the Human Cell Atlas project, directly via R/Bioconductor
Spanki ⭐ 7
Splicing analysis toolkit for RNA-SEQ
Primerseq ⭐ 7
Primer Seek in RNA-Seq. Designs RT-PCR primers that validate alternative splicing events from RNA-Seq data.
Biowardrobe ⭐ 7
BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data
2017 June Rna Seq Workshop ⭐ 7
Focused multi-day workshop covering the material needed for a successful RNA-Seq experiment.
Rna Seq Exercises ⭐ 7
Exercises for training scientists to perform some RNA-seq analyses.
Mapp ⭐ 7
🗺️ MAPP is a computational method which enables identification of binding motifs for RNA-binding proteins that shape pre-mRNA processing under specific conditions.
Knowseq ⭐ 6
KnowSeq R package
Signals ⭐ 6
Single Cell Genomes with Allele Specificity
Dturtle ⭐ 6
Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:
Socube ⭐ 6
A simple python package for doublet detection in scRNA-seq data
Scmagic ⭐ 6
Accurately annotating scRNA-seq data using two rounds of reference-based classification
Curare ⭐ 6
Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments
Autocirc ⭐ 6
A computational toolkit of fast and automatical identification of back-splice junctions of potential circular RNAs (circRNAs) from RNA-seq data.
Rnaseq_workflow ⭐ 6
snakemake workflow for bulk RNA-seq workflow using STAR-edgeR
Mcapitata_oa_developmental_gene_expression_timeseries ⭐ 6
Developmental timeseries of the reef-building coral Montipora capitata under predicted low and extreme low ocean acidification scenarios
Speaqeasy ⭐ 6
SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.
Caars ⭐ 6
CAARS: Comparative Assembly and Annotation of RNA-Seq data
Chase ⭐ 6
Chromatin Analysis & Exploration Tool
Deepsplice ⭐ 6
DeepSplice: Deep Classification of Novel Splice Junctions Revealed by RNA-seq
Pyfeat 2.x ⭐ 6
Biological Feature Representation Tool form the Sequences
Ppcseq ⭐ 6
Probabilistic outlier identification for bulk RNA sequencing data
Sargasso ⭐ 6
Sargasso disambiguates mixed-species high-throughput sequencing data.
Matataki ⭐ 6
Ultrafast mRNA Quantification software for RNA-Seq
Spritz ⭐ 6
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
Ciara_python ⭐ 6
Implementation of entropy of mixing algorithm in python
Mea ⭐ 6
Mir Magic ⭐ 6
miRNA quantification from small RNA-seq
Pipeone ⭐ 6
PipeOne: an integrative RNA-seq analysis pipeline
Plants Pipeline ⭐ 6
This project is an automated pipeline to generate annotated gene expression atlases for kingdoms of life
Tag Seq ⭐ 6
3’ Tag RNA-seq pipeline (Work in progress)
Bam Lorenz Coverage ⭐ 6
Generate Lorenz plots and Coverage plots directly from BAM files
Ipsa Nf ⭐ 5
Integrative Pipeline for Splicing Analyses (IPSA) in Nextflow
Raids ⭐ 5
Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms
Digitaldlsorter ⭐ 5
digitalDLSorteR: An R package to deconvolute bulk RNA-Seq using scRNA-Seq data
Phd Thesis ⭐ 5
My PhD thesis - "Tools and techniques for single-cell RNA sequencing data"
Imrep.gtex ⭐ 5
Scripts and commands we used in our study : Profiling immunoglobulin repertoires across multiple human tissues by RNA Sequencing
Methods ⭐ 5
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
Circminer ⭐ 5
A sensitive and fast tool for circular RNA detection from RNA-Seq data
As_analysis ⭐ 5
A complete Snakemake pipeline for detecting allele specific expression
Jaffelab ⭐ 5
R package with commonly used functions by the Jaffe lab
Muren ⭐ 5
MUREN: a Robust and Multi-reference Approach of RNA-seq Transcript Normalization
Lyric ⭐ 5
Long RNA-seq analysis workflow
Splice Q ⭐ 5
SPLICE-q -- A Python tool for genome-wide SPLIcing Efficiency quantification from RNA-seq data.
Decontaminer ⭐ 5
DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS da
Ngstips ⭐ 5
Plaqview ⭐ 5
This is a standalone interactive Shiny tool to analyze and explore single-cell RNA-seq data from human coronary artery.
Ribomethseq Nf ⭐ 5
Nextflow pipeline dedicated to RiboMethSeq data processing
Scallopadvising ⭐ 5
Clair3 Rna ⭐ 5
Clair3-RNA - long-read short variant caller for RNA sequencing data
Bento Seq ⭐ 5
Bootstrap Estimation Tool for RNA-Seq
Alaska ⭐ 5
Automated and friendly RNA-seq analysis (deprecated)
Metadatatable ⭐ 5
Work on and around an interactive metadata table for project identification
Celltalkdb ⭐ 5
A manually curated database of literature-supported ligand-receptor interactions in human and mouse
Epydoor ⭐ 5
Epitope discovery pipeline for RNA-seq
Top 10 ⭐ 5
top 10 challenges in dat science
Rawg ⭐ 5
RNA-Seq Analysis Workflow Generator
Bioinformatics_pipeline ⭐ 5
Bioinformatics Pipeline
Ribo Oddr ⭐ 5
Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs
Recount Contributions ⭐ 5
Contribute your human Illumina RNA-seq data to recount2
Genexvis ⭐ 5
An application for exploring and visualizing differential gene expression data created with DESeq2
Rnabridge Align ⭐ 5
rnabridge-align is an efficient tool to bridge paired-end RNA-seq reads
Baerhunter ⭐ 5
Genome_tracks ⭐ 5
A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.
Rediscover ⭐ 5
RNA editing discovery from NGS data.
Utr_add_extend_gtf ⭐ 5
Provided tool will add explicit 3'UTR and extends it into a valid Ensembl GTF file. It's useful for 3'RNAseq when 3' coordinates might not be as good as you expect.
Tair ⭐ 5
The Atlas of Immunoglobulin Repertoires (TheAIR)
Genocraft ⭐ 5
GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization
Scdva ⭐ 5
An R shiny based tool used for single cell RNA-seq data visualization and analysis.
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