Powering single-cell analyses in the browser with WebAssembly
Powering single-cell analyses in the browser with WebAssembly - Published in JOSS (2023)
scrnaseq
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
OUTRIDER
OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
dualrnaseq
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
efp-seq_browser
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.
dea_limma
A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.
spilterlize_integrate
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.
macrophage-regulation
Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation
bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
single-cell-training
SIB course on single cell transcriptomics by mostly using the Seurat pipeline
differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
ideal
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
SpotClean
R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
svist4get
A simple visualisation tool for genomic tracks from sequencing experiments.
rnalysis
Analyze your RNA sequencing data without writing a single line of code
aric
Accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data
scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
curare
Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments
itclust
Iterative transfer learning with neural network improves clustering and cell type classification in single-cell RNA-seq analysis
volcano3d
An R package to plot interactive three-way differential expression analysis
pram
An R/Bioconductor package to predict intergenic transcript models from RNA-seq
icetea
R/Bioconductor package for analysis of single and paired-end capped-RNAseq data (CAGE/RAMPAGE/MAPCap)
digitaldlsorter
digitalDLSorteR: An R package to deconvolute bulk RNA-Seq using scRNA-Seq data
DEGreport
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
cellama
Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports
APAlyzer
APAlyzer is a toolkit for bioinformatic analysis of alternative polyadenylation (APA) events using RNA sequencing data. Our main approach is the comparison of sequencing reads in regions demarcated by high-quality polyadenylation sites (PASs) annotated in the PolyA_DB database (https://exon.apps.wistar.org/PolyA_DB/v3/). The current version (v3.0) uses RNA-seq data to examine APA events in 3’ untranslated regions (3’UTRs) and in introns. The coding regions are used for gene expression calculation.
https://github.com/csoneson/armor
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
https://github.com/broadinstitute/genepy
Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python
https://github.com/bioconductor/orchestratingsinglecellanalysis
Content for the OSCA Book.
rseb
An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.
https://github.com/ahmedmoustafa/gene-expression-datasets
Collection of gene expression datasets
https://github.com/broadinstitute/temporal-rna-seq-deconvolution
Package for temporal deconvolution of bulk RNA-seq samples using SVI
rnaseq_pipeline
RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
https://github.com/daisybio/DysRegNet_package
Inferring patient-specific regulatory alterations
https://github.com/broadinstitute/celligner2
A new version of the celligner package using VAEs. Inspired from the Theis lab's scArches.
zarp-cli
A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
enrichment_analysis
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
helical
A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.
RAIDS
Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms
tucca-rna-seq
Tufts University Center for Cellular Agriculture's RNA-Seq Workflow for Cellular Agriculture Projects
hamrlnc
High-throughput pipeline for modified mRNA annotation and long non-coding RNA annotation
https://github.com/bvieth/powsimr
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.
https://github.com/bgeedb/bgee_pipeline
Source code of the Bgee pipeline used to build the Bgee database
genome_tracks
A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.
dseqr
single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.
sofur
Worflow to detect, annotate, filter and vizualize somatic fusions from stranded paired-end RNA-seq from Illumina instruments.
denovotranscript
A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq
pyigmap
[UNDER DEVELOPMENT] Pipeline for mapping and annotating T- and B-cell receptor gene rearrangement sequences
https://github.com/bimberlab/nimble-aligner
nimble-aligner is the backend for nimble, a tool that executes lightweight, flexible alignments to generate supplemental alignment data
ccsinglecell
A project focused on using single-cell RNA sequencing data (scRNA-seq) and pseudo time to improve colon cancer diagnosis and outcomes.
xpresspipe
An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data
https://github.com/angrymaciek/mapp
🗺️ MAPP is a computational method which enables identification of binding motifs for RNA-binding proteins that shape pre-mRNA processing under specific conditions.
futuriandge
This is a personal project focused on creating uniformal pipeline for processing RNA-seq data with the end goal to create a .Rdata object which can be imported into R/Shiny app for downstream analysis and hypothesis testing.
easybio
Comprehensive Single-Cell Annotation and Transcriptomic Analysis Toolkit
https://github.com/bmascat/rna-seq-proteomics-pipeline
Multi-omics analysis of LFQ proteomics and transcriptomics of an ALMS1 gene knockout cell model after TGF-B pathway stimulation.
pytximport
Feature-rich Python implementation of the tximport package for gene count estimation.
https://github.com/bleekerlab/shiny_rnaseq_app
An Shiny application to explore RNA-seq results produced from the laboratory on tomato. Web application is private under password protection (please request access).