Pinned Repositories
clip_pipeline
CLIP pipeline
COPILOT
Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline as the input of copilot.
DeepRiPe
liam
PARpipe
Complete analysis pipeline for PAR-CLIP data
Riboseq_Pipeline
This is the Lab's standard Ribo-seq processing pipeline, a snakemake workflow and some R scripts.
RiboseQC
Pipeline for Quality Control of Ribo-Seq data, selection of P-site offsets, and codon usage statistics.
RiboTaper
SEMITONES
SEMITONES_paper
ohlerlab's Repositories
ohlerlab/DeepRiPe
ohlerlab/RiboseQC
Pipeline for Quality Control of Ribo-Seq data, selection of P-site offsets, and codon usage statistics.
ohlerlab/COPILOT
Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline as the input of copilot.
ohlerlab/PARpipe
Complete analysis pipeline for PAR-CLIP data
ohlerlab/SEMITONES
ohlerlab/Riboseq_Pipeline
This is the Lab's standard Ribo-seq processing pipeline, a snakemake workflow and some R scripts.
ohlerlab/liam
ohlerlab/clip_pipeline
CLIP pipeline
ohlerlab/mlcis
ohlerlab/SEMITONES_paper
ohlerlab/cortexomics
This is the omics section of the Neocortical Development project, collaboration with Matthias Kraushar
ohlerlab/liam_manuscript_reproducibility
ohlerlab/omniCLIP
omniCLIP is a CLIP-Seq peak caller
ohlerlab/RiboStan
Quantification And Analysis of Ribo-seq
ohlerlab/RiboTaper
ohlerlab/scKB
Use kallisto and bustools to call the gene-cell matrix for both spliced and unspliced transcripts of scRNA-seq
ohlerlab/bioconda-recipes
Conda recipes for the bioconda channel.
ohlerlab/Cseq-Simulator
Cseq-Simulator is a pipeline for realistic RNA-Clip simulations. It mimics key steps of Clip protocols and allows with user provided profiles to simulate any diagnostic event distribution (RBPs). Furthermore, Cseq-Simulator is very individual and lets the user provide a list of RBP binding sites or transcipt abundance profiles.
ohlerlab/FootprintPipeline
Pipeline to find transcription factor footprints in DNase-seq or ATAC-seq datasets
ohlerlab/galaxy-rna-workbench
Galaxy RNA workbench
ohlerlab/galaxytools
:microscope::books: Galaxy Tool wrappers
ohlerlab/JAMM
JAMM Peak Finder for Sequencing Datasets
ohlerlab/liam_challenge_reproducibility
ohlerlab/McEnhancer
Source code and results for McEnhancer: Predicting gene expression via semi-supervised assignment of enhancers to target genes
ohlerlab/ORFquant
An R package for Splice-aware quantification of translation using Ribo-seq data
ohlerlab/TimelessFlex
TimelessFlex - A flexible framework for investigating chromatin state trajectories