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Search results for rna seq
rna-seq
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386 search results found
Itclust
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39
Iterative transfer learning with neural network improves clustering and cell type classification in single-cell RNA-seq analysis
Dgca
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38
Differential Gene Correlation Analysis
Tcc Gui
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37
📊 Graphical User Interface for TCC package
Cellsnp
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37
Pileup biallelic SNPs from single-cell and bulk RNA-seq data
Dee2
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37
Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
Pinfish
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36
Tools to annotate genomes using long read transcriptomics data
Scribe Py
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36
Regulatory networks with Direct Information in python
Tdm
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36
R package for normalizing RNA-seq data to make them comparable to microarray data.
Squid
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36
SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
Genome Annotation Pipeline
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36
Genome annotation pipeline
Haystack_bio
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35
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
Peca
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35
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
Grape Nf
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35
An automated RNA-seq pipeline using Nextflow
Pipeline Nanopore Ref Isoforms
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35
Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools
Cicero
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34
CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
Picardmetrics
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34
🚦 Run Picard on BAM files and collate 90 metrics into one file.
Differentialabundance
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34
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
Datest
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34
Compare different differential abundance and expression methods
Spatialtranscriptomics
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34
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Brie
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34
BRIE: Bayesian Regression for Isoform Estimate in Single Cells
Circrna
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32
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
Ngs_pipeline
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31
Exome/Capture/RNASeq Pipeline Implementation using snakemake
Rnadeseq
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31
Differential gene expression analysis and pathway analysis of RNAseq data
Reademption
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31
A pipeline for the computational evaluation of RNA-Seq data
Transabyss
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30
de novo assembly of RNA-seq data using ABySS
Liqa
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30
Long-read Isoform Quantification and Analysis
Ngs
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30
Next-Gen Sequencing tools from the Horvath Lab
Grein
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30
GREIN : GEO RNA-seq Experiments Interactive Navigator
Pygtftk
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30
A python package and a set of shell commands to handle GTF files
Metaomgraph
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30
MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets
Workshop Rnaseq
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30
Workshop • Analysis of RNA-seq data
Rnaseq_titration_results
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29
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
Virtus
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28
A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
Rnaseq
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28
RNASeq pipeline
Combat Seq
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28
Batch effect adjustment based on negative binomial regression for RNA sequencing count data
Wiggleplotr
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28
A small R package to make sequencing read coverage plots in R.
Volcano3d
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28
An R package to plot interactive three-way differential expression analysis
Ideal
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28
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
Bird
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27
Big data Regression for predicting DNase I hypersensitivity
Scedar
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27
Single-cell exploratory data analysis for RNA-Seq
Soapdenovo Trans
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27
SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.
Expressionmatrix2
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27
Software for exploration of gene expression data from single-cell RNA sequencing.
Biotoolbox
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27
Tools for querying and analysis of genomic data
Deepstats
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27
deepStats: a stastitical toolbox for deeptools and genomic signals
Smallrnaseq
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26
small rna-seq analysis package
Pisces
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26
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
Zarp
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26
Zavolan-Lab Automated RNA-Seq Pipeline
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.
Annogesic
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25
ANNOgesic - A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes
Mudskipper
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25
A tool for projecting genomic alignments to transcriptomic coordinates
Teaching
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25
This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.
Pipeliner
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25
A flexible Nextflow-based framework for the definition of sequencing data processing pipelines
Pyrpipe
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25
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
Scib Reproducibility
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25
Additional code and analysis from the single-cell integration benchmarking project
Tape
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25
Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)
Vigen
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24
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
Rnatoy
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24
A proof of concept RNA-Seq pipeline with Nextflow
M3drop
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24
Asap
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24
ASAP : Automated Single-cell Analysis Pipeline
Rum
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24
RNA-Seq Unified Mapper
Dapars2
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24
Dynamics analysis of Alternative PolyAdenylation from RNA-seq
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
Splam
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24
✂️ Deep learning-based splice site predictor that improves spliced alignments
Idea
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23
Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
Rnavar
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23
gatk4 RNA variant calling pipeline
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.
Fishpond
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23
Differential expression and allelic analysis, nonparametric statistics
Starchip
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23
Detection of Circular RNA and Fusions from RNA-Seq
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.
Alpine
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22
Modeling and correcting fragment sequence bias for RNA-seq
Popscle
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22
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
Pipeline Pinfish Analysis
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22
Pipeline for annotating genomes using long read transcriptomics data with pinfish
Fraser
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22
FRASER - Find RAre Splicing Events in 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.
Sgtk
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21
Example of SGTK application for E.coli dataset:
Splicejam
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21
Sashimi plots for RNA-seq data using detected transcripts
Pm4ngs
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21
Project Manager for NGS data analysis
Degreport
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21
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
Guessmylt
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20
An efficient way to guess the library type of your RNA-Seq data.
Rna Seq Snakemake
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20
Snakemake based pipeline for RNA-Seq analysis
Rnaseq Nf
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20
RNAseq analysis pipeline
Mop2
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20
Master of Pores 2
Conekt
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20
CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.
Enrichment Analysis
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20
From RNA-seq raw reads to enriched pathways by DEGs
Pigx_rnaseq
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19
Pipeline for RNAseq
Pipeline Nanopore Denovo Isoforms
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19
Pipeline for de novo clustering of long transcriptomic reads
Deepcycle
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19
Cell cycle inference in single-cell RNA-seq
Ggr Cwl
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19
CWL tools and workflows for GGR
Heatmapgenerator
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19
Cross-platform GUI desktop application for making biological heatmaps
Rnaseq Pipeline
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18
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Sctcrseq
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18
Processing of single cell RNAseq data for the recovery of TCRs in python
Rnasplice
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18
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
Slamdunk
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18
Streamlining SLAM-seq analysis with ultra-high sensitivity
Tailseeker
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18
Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer
Rna Seq
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18
A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
Agouti
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18
Annotated Genome Optimization Using Transcriptome Information
Devcellpy
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18
devCellPy is a Python package designed for hierarchical multilayered classification of cells based on single-cell RNA-sequencing.
Lapa
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18
Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
Microscope
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17
ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps
Related Searches
R Rna Seq (194)
Python Rna Seq (178)
Bioinformatics Rna Seq (141)
Pipeline Rna Seq (111)
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