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caleblareau Goto Github PK
Name: Caleb Lareau
Type: User
Company: Memorial Sloan Kettering Cancer Center
Twitter: caleblareau
Location: New York, NY
Blog: https://clareaulab.com
Caleb Lareau's Projects
eclip_sars_cov2_trim
CL Repository for processing CLIP data from SARS COV2
errorcorrect_10xatac_barcodes
Simple utility python script for processing R1/R2/R3 10x ATAC fastq files and error correcting them.
frank-bulk-atac-rescue
CL repo for python parsing bulk atac data from weird demultiplexing
gchromvar
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
genomic-annotations
Single place for common genomic annotations that I keep manually re-generating
gmap-gsnap
*UNMAINTAINED and OUTDATED*: This was an inofficial archive of GMAP-GSNAP releases. Please use the original website for current versions of the source code.
greenleaf10x
Analysis/Summary statistics of Greenleaf Lab 10X Data
grna_table_to_bedfile
Create bed file for extracting reads from perturb experiments
hca_scatac_processing
Repository for parsing various scATAC data scripts
hemebulkrna
Human Heme RNA-Seq data aligned to 10X gtf
hemebulkrna_10xmap
Human Heme Bulk RNA aligned via 10X pipeline
hhv6-reactivation
Repository for analyses of HHV-6 reactivation using genomics
hhv6_bwa
Repositories for HHV-6 genomes indexed by BWA
hisnpper
Toolkit for annotating bam files with haplotype SNVs
iheatmapr
Complex, interactive heatmaps in R
immgen-tsne-revisions
Repository for revisions for ImmGen tSNE
immgen_final
Final analyses for ImmGen Paper
immune_cell_signature_genes
Repository for signature genes from Immune Cell Atlas
immunology-206-atacseq
Repository for ATAC-seq teaching materials for Immunology 206 | March 2, 2023
indrop
An R package for basic indrop analyses and data handling
jon-ep-loops
K562 loops for Jon
k562-hichip
Simple workflow for analyzing multiple HiChIP replicate data with `diffloop`
kite_for_dummies
Reminders to myself because I keep forgetting how to use kite efficiently
lapels
Lapels: remap and annotate read alignments against in silico (pseudo) genomes
lin28b-bcl11a-hbf
CL analysis for Ani's project
lmmlite
Simple port of pylmm: linear mixed models for GWAS
maegatk
Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
mgatk
mgatk: mitochondrial genome analysis toolkit
mitoblacklist
Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome
motifmatchr
Fast motif matching in R
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