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Search results for python transcriptomics

transcriptomics x

36 search results found

Scanpy ⭐ 1,753

Single-cell analysis in Python. Scales to >1M cells.

Pydeseq2 ⭐ 470

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Pyscenic ⭐ 321

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

Starfish ⭐ 220

starfish: unified pipelines for image-based transcriptomics

Single cell perturbation prediction

Diffxpy ⭐ 157

Differential expression analysis for single-cell RNA-seq data.

Identification of differential RNA modifications from nanopore direct RNA sequencing

Rnalysis ⭐ 114

RNA sequencing analysis software

Decoupler Py ⭐ 112

Python package to perform enrichment analysis from omics data.

Isoquant ⭐ 98

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Pychopper ⭐ 74

A tool to identify, orient, trim and rescue full length cDNA reads

just annotate it, dammit!

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.

Pyrovelocity ⭐ 31

𝒫robabilistic modeling of RNA velocity ⬱

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

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.

Chromoformer ⭐ 24

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

Nmdc Schema ⭐ 23

This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.

Pipeline Pinfish Analysis ⭐ 22

Pipeline for annotating genomes using long read transcriptomics data with pinfish

(formerly eelpond) an automated RNA-Seq workflow system

Pipeline Nanopore Denovo Isoforms ⭐ 19

Pipeline for de novo clustering of long transcriptomic reads

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Enrich_omics ⭐ 15

A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)

Isotools ⭐ 15

IsoTools is a python module for Long Read Transcriptome Sequencing (LRTS) analysis.

Digitalcellsorter ⭐ 14

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

Stabilized Ica ⭐ 12

This repository proposes a python implementation of a stabilized ICA algorithm

Reaction Inclusion by Parsimony and Transcript Distribution

Personalized_regression ⭐ 8

Personalized Regression

Bgee_pipeline ⭐ 8

Source code of the Bgee pipeline used to build the Bgee database

Singlecellhaystack Py ⭐ 8

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).

Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)

Glue Genes ⭐ 7

glue for genomics and transcriptomics

A network-based approach for exon set enrichment

Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments

Spicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data

CAARS: Comparative Assembly and Annotation of RNA-Seq data

Long RNA-seq analysis workflow

An awesome Oxford Nanopore Pipeline for direct RNA-sequencing

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