94 Open source projects that are alternatives of or similar to pychopper

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Reference-based transcript discovery from long RNA read

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

A versatile sequenced read processor for nanopore direct RNA sequencing

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

Multi-omics analysis protocols by Lyu.

Differential Gene Correlation Analysis

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

A fast tool for hybrid genome assembly of long and short reads

Next-Gen Sequencing tools from the Horvath Lab

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

CellNet: network biology applied to stem cell engineering

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

MERlin is an extensible analysis pipeline applied to decoding MERFISH data

Dynamical systems methods for RNA velocity analysis

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Version 2.1.0 released

A curated list of awesome nanopore analysis tools.

An accurate and ultra-fast hybrid genome assembler

Deep Learning based cell composition analysis with Scaden.

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

A proof of concept RNA-Seq pipeline with Nextflow

PEPPER-Margin-DeepVariant

Feature extraction algorithm for genomic data

Fast in-silico normalization algorithm for NGS data

GREIN : GEO RNA-seq Experiments Interactive Navigator

Research release basecalling models and configurations

scRNA-seq data visualization from scrattch

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

RNASeq pipeline

A graphical user interface for distributed data processing of high throughput genomics

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

Scripts to import your FeatureCounts output into DEXSeq

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

Fast and accurate gene fusion detection from RNA-Seq data

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.

Processing of single cell RNAseq data for the recovery of TCRs in python

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

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

Streamlining SLAM-seq analysis with ultra-high sensitivity

Single cell analysis in the browser

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

FEELnc : FlExible Extraction of LncRNA

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

An automated RNA-seq pipeline using Nextflow

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

📊 Graphical User Interface for TCC package

Porting DESeq2 and DEXSeq into python via rpy2