Pinned Repositories
bamMotifSearcher
Find reads in a bam file that contain a given sequence (can contain degenerate bases)
bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
bioconda-recipes
Conda recipes for the bioconda channel.
bsub_jupyter
Connect to a LSF main node directly or trough a ssh jump node, launch a jupyter notebook via bsub and open automatically a tunnel. The name of the connection can be used to reestablish the connection later or to terminate it.
bug-free-disco
chip-seq-pipeline2
chip_tutorial
Clinder
conda-wdls
WDLs and conda environments for running genomic analyses on a HPC using conda (e.g. instead of docker)
kclem's Repositories
kclem/bamMotifSearcher
Find reads in a bam file that contain a given sequence (can contain degenerate bases)
kclem/bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
kclem/bioconda-recipes
Conda recipes for the bioconda channel.
kclem/bsub_jupyter
Connect to a LSF main node directly or trough a ssh jump node, launch a jupyter notebook via bsub and open automatically a tunnel. The name of the connection can be used to reestablish the connection later or to terminate it.
kclem/bug-free-disco
kclem/chip-seq-pipeline2
kclem/chip_tutorial
kclem/Clinder
kclem/conda-wdls
WDLs and conda environments for running genomic analyses on a HPC using conda (e.g. instead of docker)
kclem/CRISPRatac
kclem/CRISPResso
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
kclem/cutadapt
Cutadapt removes adapter sequences from sequencing reads
kclem/dockstore-tool-bamstats
A repo for the BAMStats command, used as the tutorial for Dockstore
kclem/GEM
Genome Editing Metadata API
kclem/getClinvar
kclem/guideFinder
kclem/insertion_checker
kclem/MeKit
kclem/methylation-workflow
kclem/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
kclem/PEM-Q
a pipeline to process data of PEM-seq or data similar, which is more comprehensive than superQ
kclem/shinydemo
kclem/simple_python_package_setuptools
Simple python package to demonstrate package imports with setuptools
kclem/simulateIndels
kclem/strelka
Strelka2 germline and somatic small variant caller
kclem/suffix-tree
implementation of how to construct suffix tree
kclem/test_project