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Search results for python rna seq
python
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rna-seq
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112 search results found
Deeptools
⭐
644
Tools to process and analyze deep sequencing data.
Rna Seq Analysis
⭐
614
RNAseq analysis notes from Ming Tang
Pydeseq2
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470
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Snakepipes
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359
Customizable workflows based on snakemake and python for the analysis of NGS data
Rna Seq Star Deseq2
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282
RNA-seq workflow using STAR and DESeq2
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.
Xpore
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122
Identification of differential RNA modifications from nanopore direct RNA sequencing
Fusioncatcher
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117
Finder of Somatic Fusion Genes in RNA-seq data
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
Isoquant
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98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Pipeline Transcriptome De
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95
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
Spark
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81
Publication quality NGS track plotting
Pychopper
⭐
74
A tool to identify, orient, trim and rescue full length cDNA reads
Scnym
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71
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
Diffexpr
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67
Porting DESeq2 into python via rpy2
Trinity_ctat
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63
Rna Seq Kallisto Sleuth
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63
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
Lorean
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62
Long Reads Annotation pipeline
Covid 19 Rna Seq Datasets
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61
A repository for sharing information on available COVID-19 RNA-Seq datasets
Snakefiles
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58
🐍 Snakefiles for common RNA-seq data analysis workflows.
Poreplex
⭐
51
A versatile sequenced read processor for nanopore direct RNA sequencing
Agfusion
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46
Python package to annotate and visualize gene fusions.
Pipeliner
⭐
44
An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
Cell2cell
⭐
44
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
Finder
⭐
44
A fully automated gene annotator from RNA-Seq expression data
Metasra Pipeline
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42
MetaSRA: normalized sample-specific metadata for the Sequence Read Archive
Dapars
⭐
41
DaPars(Dynamic analysis of Alternative PolyAdenylation from RNA-seq)
Cellxgene Gateway
⭐
40
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
Sprint
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40
SNP-free RNA editing Identification Toolkit
Scaden
⭐
40
Deep Learning based cell composition analysis with Scaden.
Cellsnp
⭐
37
Pileup biallelic SNPs from single-cell and bulk RNA-seq data
Scribe Py
⭐
36
Regulatory networks with Direct Information in python
Pipeline Nanopore Ref Isoforms
⭐
35
Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools
Brie
⭐
34
BRIE: Bayesian Regression for Isoform Estimate in Single Cells
Reademption
⭐
31
A pipeline for the computational evaluation of RNA-Seq data
Ngs_pipeline
⭐
31
Exome/Capture/RNASeq Pipeline Implementation using snakemake
Pygtftk
⭐
30
A python package and a set of shell commands to handle GTF files
Transabyss
⭐
30
de novo assembly of RNA-seq data using ABySS
Ngs
⭐
30
Next-Gen Sequencing tools from the Horvath Lab
Liqa
⭐
30
Long-read Isoform Quantification and Analysis
Zarp
⭐
26
Zavolan-Lab Automated RNA-Seq Pipeline
Smallrnaseq
⭐
26
small rna-seq analysis package
Pisces
⭐
26
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
Annogesic
⭐
25
ANNOgesic - A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes
Pyrpipe
⭐
25
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
Teaching
⭐
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.
Dapars2
⭐
24
Dynamics analysis of Alternative PolyAdenylation from RNA-seq
Pipeline Pinfish Analysis
⭐
22
Pipeline for annotating genomes using long read transcriptomics data with pinfish
Pm4ngs
⭐
21
Project Manager for NGS data analysis
Guessmylt
⭐
20
An efficient way to guess the library type of your RNA-Seq data.
Conekt
⭐
20
CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.
Deepcycle
⭐
19
Cell cycle inference in single-cell RNA-seq
Pipeline Nanopore Denovo Isoforms
⭐
19
Pipeline for de novo clustering of long transcriptomic reads
Pigx_rnaseq
⭐
19
Pipeline for RNAseq
Rnaseq Pipeline
⭐
18
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Sctcrseq
⭐
18
Processing of single cell RNAseq data for the recovery of TCRs in python
Agouti
⭐
18
Annotated Genome Optimization Using Transcriptome Information
Slamdunk
⭐
18
Streamlining SLAM-seq analysis with ultra-high sensitivity
Open_pipelines
⭐
17
Pipelines for NGS data preprocessing by the Bock lab and friends
Iris
⭐
17
IRIS: Isoform peptides from RNA splicing for Immunotherapy target Screening
Msisensor Rna
⭐
15
MSIsensor-RNA: Microsatellite instability detection using RNA sequencing data
Subread_to_dexseq
⭐
15
A way to use FeatureCounts output for DEXSeq
Velodyn
⭐
15
Dynamical systems methods for RNA velocity analysis
Pyflow Rnaseq
⭐
15
RNAseq pipeline based on snakemake
Rnaseqreadsimulator
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14
RNASeqReadSimulator is a simple tool to generate simulated single-end or paired-end RNA-Seq reads.
Pegasas
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14
Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)
Pavfinder
⭐
14
🔍 Post Assembly Variants Finder
Gdc Rnaseq Tool
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14
Tool to download/merge RNASeq data from the GDC Portal in matrices identified by TCGA barcode
Lr Splitpipe
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13
Demultiplexing and debarcoding tool designed for LR-Split-seq data.
Toolkit
⭐
13
A toolkit for NGS analysis with Python
Ymp
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13
Flexible omics pipeline
Transindel
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13
Indel caller for DNA-seq or RNA-seq
Apaeval
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13
Community effort to evaluate computational methods for the detection and quantification of poly(A) sites and estimating their differential usage across RNA-seq samples
Chimerate
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12
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
Phenotypexpression
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11
Subclassification of disease states based on the intersection of literature and expression
Couplednmf
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11
Coupled clustering of single cell genomic data
Xpresspipe
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11
An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data
Rna Combine
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11
RNA-seq data comprehensive data analysis toolbox
Tag Based_rnaseq
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10
Cost-efficient genome-wide gene expression profiling
Dl Based Tumor Classification
⭐
10
Deep Learning Based Tumor Type Classification Using Gene Expression Data
Ursm
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10
A Unified RNA Sequencing Model (URSM) for joint analysis of single cell and bulk RNA-seq data.
Tostadas
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10
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
Enrichment_analysis
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10
A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.
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.
Trackcluster
⭐
9
An analysis pipeline for Nanopore direct-RNA sequencing
Umitools
⭐
9
A toolset for handling sequencing data with unique molecular identifiers (UMIs)
Rnaseq Pipeline
⭐
9
RNASeq-Pipeline for Quantification and Enrichment Analysis
Star Seqr
⭐
9
RNA Fusion Detection and Quantification
Kakapo
⭐
8
A tool to extract and annotate genes from raw RNA-seq reads.
Nextgenseq_pipeline
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8
Exome/Capture/RNASeq Pipeline Implementation using snakemake
Captus
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8
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
Bgee_pipeline
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8
Source code of the Bgee pipeline used to build the Bgee database
Rna Seek
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8
A comprehensive quality-control and quantification RNA-seq pipeline
Spanki
⭐
7
Splicing analysis toolkit for RNA-SEQ
Scmmd
⭐
7
Maximum mean discrepancy comparisons for single cell profiling experiments
Nease
⭐
7
A network-based approach for exon set enrichment
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.
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