Pinned Repositories
gdc_bam_library_exomekit_docker
Melanomas-ImmuneResistance-2019
This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources of T cell exclusion linked to immunotherapy clinical outcomes".
microbiome_helper
A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
scOh
Single Cell Atlas - PDAC
Single-cell-multi-omic-profiling-of-glioblastoma-associated-myeloid-cells
Single-cell multi-omic profiling of glioblastoma-associated myeloid cells
merckey's Repositories
merckey/Single-cell-multi-omic-profiling-of-glioblastoma-associated-myeloid-cells
Single-cell multi-omic profiling of glioblastoma-associated myeloid cells
merckey/2022-July-Advanced-Topics-in-Single-Cell-RNA-Seq-ATAC
merckey/2022-July-Single-Cell-RNA-Seq-Analysis
merckey/2022-March-Advanced-Topics-in-Single-Cell-RNA-Seq-VDJ
An in-depth look at VDJ analysis with single cell RNA-Seq data. Participants must already be familiar with single cell RNA-Seq analysis.
merckey/2022-March-Single-Cell-RNA-Seq-Analysis
A workshop for biologists preparing to run their first single cell RNA Seq experiment. Participants should have some command line and R experience to participate successfully. We recommend our introductory courses for beginners!
merckey/atacseq
ATAC-seq peak-calling, QC and differential analysis pipeline
merckey/AutomaticCellTypeIdentification
merckey/CCI
Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information
merckey/COVID19-scATAC-seq
merckey/GenomeScienceCourse
Scripts and data for Genome Science course at HKU
merckey/gistic2
Genomic Identification of Significant Targets in Cancer (GISTIC), version 2
merckey/gsea-cli-scripts
Scripts for running GSEA at the command line
merckey/HPA-SingleCellType
merckey/MALDI_HDC-SC
merckey/map_flu_serum_Perth2009_H3_HA
mutational antigenic profiling of Perth/2009 H3 HA against serum
merckey/MCDA
Systematic identification of cell fate regulatory programs using a single-cell atlas of mouse development
merckey/Melanoma_Brain_Metastasis
Dissecting the treatment-naïve ecosystem of human melanoma brain metastasis
merckey/mirna
microRNA profiling pipeline
merckey/NicheNet_LiverCellAtlas
Scripts used for the Differential NicheNet analyses in the Liver Atlas paper Guilliams et al., Cell 2022
merckey/RefConstruction_supervisedCelltyping
Source code for "Evaluation of some aspects in supervised cell type identification for single-cell RNA-seq: classifier, feature selection, and reference construction".
merckey/sc-atac-seq-pipeline
ATAC-seq pipelines for HuBMAP
merckey/scRNAaltas_TNBC_mm
merckey/seqplots
:chart_with_upwards_trend:SeqPlots - An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
merckey/sigminer
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
merckey/smrnaseq
A small-RNA sequencing analysis pipeline
merckey/SPATAwrappers
Additional SPATA functions
merckey/TelescopeEncode
merckey/thebaud_lung_BPD
R Notebooks for Hurskainen & Mizikova et al., 2020
merckey/training-material
A collection of Galaxy-related training material
merckey/UnivCambridge_ScRnaSeqIntro_Feb2022