CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
☆11May 20, 2026Updated this week
Alternatives and similar repositories for cageseq
Users that are interested in cageseq are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCF…☆11Feb 3, 2021Updated 5 years ago
- CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.☆24Jan 15, 2026Updated 4 months ago
- k-mer similarity analysis pipeline☆22Apr 30, 2026Updated 3 weeks ago
- Please consider using/contributing to https://github.com/nf-core/sarek☆18Jan 3, 2019Updated 7 years ago
- Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.☆13Jun 3, 2025Updated 11 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Allele-Specific Quantification of Structural Variations in Cancer Genomes☆18Mar 5, 2019Updated 7 years ago
- Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)☆28Apr 30, 2026Updated 3 weeks ago
- MNase-seq analysis pipeline using BWA and DANPOS2.☆13Feb 23, 2026Updated 3 months ago
- Code base for profiling highly replicated differential gene expression RNA-seq.☆11Dec 13, 2021Updated 4 years ago
- Localization of transcribed enhancers and quntification of their usage from the initiation sites of bidirectionally transcribed loci☆14Dec 19, 2024Updated last year
- UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets☆34Apr 4, 2025Updated last year
- An analysis pipeline for Nanostring nCounter expression data.☆18Apr 30, 2026Updated 3 weeks ago
- 从科学基金共享服务网爬取所有公开的国自然结题项目☆18Sep 8, 2017Updated 8 years ago
- Nascent Transcription Processing Pipeline☆22Apr 30, 2026Updated 3 weeks ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- ☆20Mar 13, 2026Updated 2 months ago
- DIAMOND online documentation☆10Sep 2, 2020Updated 5 years ago
- Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.☆18Jun 3, 2025Updated 11 months ago
- Clair3-Trio: variant calling in trio using Nanopore long-reads☆16Apr 18, 2024Updated 2 years ago
- singleCellNet in Python☆16Feb 25, 2026Updated 2 months ago
- Decomposition-based peak identification, which find peaks across a large number of TSS (transcription starting site) profiles☆15Aug 3, 2017Updated 8 years ago
- Determining tandem repeat lengths using raw nanopore signals.☆15Sep 11, 2023Updated 2 years ago
- Assembly and intrahost / low-frequency variant calling for viral samples☆15Feb 12, 2020Updated 6 years ago
- A pipeline to investigate horizontal gene transfer from NGS data☆26Apr 30, 2026Updated 3 weeks ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.☆25Jun 26, 2025Updated 10 months ago
- Nanopore raw signal repeat detection pipeline☆45Mar 17, 2023Updated 3 years ago
- B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework☆77May 15, 2026Updated last week
- Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.☆24Jun 3, 2025Updated 11 months ago
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…☆24Apr 30, 2026Updated 3 weeks ago
- ☆35Apr 20, 2026Updated last month
- Classifier of pathogenic non-coding variants in Mendelian diseases☆11Feb 6, 2020Updated 6 years ago
- single cell analysis of treatment naive and treated human PDAC☆25May 27, 2022Updated 3 years ago
- Collection of Sphinx extensions similar to (but more flexible than) numpydoc☆12Updated this week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Converts bam or cram files to fastq format and does quality control.☆31May 13, 2026Updated last week
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- ☆30Sep 11, 2025Updated 8 months ago
- An insertion caller for Illumina paired-end WGS data.☆24Aug 22, 2025Updated 9 months ago
- ☆23May 15, 2026Updated last week
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆66Apr 30, 2026Updated 3 weeks ago
- HiGlass track for displaying arcs between disconnected regions☆10Dec 13, 2022Updated 3 years ago