In-progress projects at Harvard School of Public Health Bioinformatics Core
HTML Python Perl R Clojure Shell Other
Latest commit 851d4ec Feb 23, 2017 @mjsteinbaugh mjsteinbaugh Update before meeting
Permalink
Failed to load latest commit information.
ab_450K_repeats/scripts add 450K scripts, update lk_FOY, add aw_NFKB scripts Jan 23, 2014
ab_nucmito/scripts merge in Illumina annotations to final probelist Dec 8, 2015
ab_rrbs_comparison/scripts use correct genome build from biomart Mar 17, 2015
ab_teloprobes/scripts final version of script Aug 7, 2015
aw_NFKB/scripts wagers mogene script with interaction terms in limma Jan 30, 2014
aw_NMF_proteomics adjust to use non-batch corrected data for limma Mar 31, 2016
aw_rnaseq_dev add 450K scripts, update lk_FOY, add aw_NFKB scripts Jan 23, 2014
ay_linkertrim Pick useful verification targets based on multiple criteria Jan 25, 2012
ben_trap_pilot Project cleanup for completed projects. Jun 1, 2013
bh_assembly/scripts script to look at COGs Dec 10, 2015
breault_betacatenin_rnaseq adding report markdowns for all my completed/nearly completed consults Sep 17, 2015
breault_bmal_rnaseq Adding scripts for breault, macklis, teplyuk, and weiner consults Mar 22, 2016
ci_gut_rnaseq/summary add Xist analysis to pca Dec 13, 2016
dg_cardiac_timeseries/scripts trial version of deseq analysis to find genes which vary over time Mar 17, 2015
dr_mouseexome Updated scripts for re-running analyses and CRAM compressing finished… Jun 17, 2014
ds_HIF1_secreted_factors/scripts First commit after reorg Jun 11, 2013
ds_PTGIR_promoter/scripts NMF analysis added Aug 9, 2013
ds_pathprint_lab_cells/scripts First commit after reorg Jun 11, 2013
dt_leukemias/scripts Tenen analysis Dec 18, 2013
ea_ibd Post process cufflinks transcript output, providing summary details o… Sep 19, 2011
flanagan_IR_rnaseq adding report markdowns for all my completed/nearly completed consults Sep 17, 2015
giab_somatic Use GiaB 3.2.2 calls for NA24385/NA12878 truth set Jun 17, 2016
gu_rnaseq updated config Sep 12, 2016
gvcf_validation Plot comparisons between gVCF and coverage based validations Jun 24, 2016
henske_miR21_fxn Adding scripts for henske analyses and slack analysis to github Oct 13, 2016
henske_tsc2_rnaseq Adding scripts for henske analyses and slack analysis to github Oct 13, 2016
hoche_chipseq Project cleanup for completed projects. Jun 1, 2013
hochedlinger_rnaseq Mass update of legacy information from previous projects. Jun 3, 2013
hoechedlinger_chipseq Mass update of legacy information from previous projects. Jun 3, 2013
jg_potoroo Cleaup. Sep 28, 2012
jl_hiv Updated scripts for re-running analyses and CRAM compressing finished… Jun 17, 2014
jl_mirna_kmer Added .gitignore. Nov 20, 2013
js_transposon Flexible UMI handling for barcode schemes Feb 22, 2017
jw_rnaseq/summary QC and RNAseq Nov 15, 2016
jz_giab Improvements on error reporting and parallelization for illumina vari… Jul 3, 2013
kantor_asthma_rnaseq Initialize asthma project. Nov 26, 2013
kc_rrbs/scripts First commit after reorg Jun 11, 2013
kclarke_colon_biopsies/scripts final version of kclarke analysis Jun 25, 2013
kobzik-rrbs/scripts add excel file output Jun 6, 2016
kobzik_influenza Updating some older projects. Aug 24, 2013
kraft_wgs Added scripts used to annotate the genomes. Jun 3, 2013
legall_ocwieja_pacbio Update Pacbio_workflow_analysis.md Dec 3, 2016
lg_AOF2_knockout_analysis/scripts First commit after reorg Jun 11, 2013
lg_bone_development/scripts First commit after reorg Jun 11, 2013
lieberman_mirna Updating some older projects. Aug 24, 2013
ljg_cardiac_rnaseq/scripts slurm command subbed,environment vars global Jun 17, 2014
lk_450k/scripts add in a few old scripts Dec 8, 2015
lk_FOY add in a few old scripts Dec 8, 2015
lk_rrbs/scripts/RRBS_methylkit First commit after reorg Jun 11, 2013
lr_motor_neurons/scripts/FACS_sorted_MNs_from_MNs-AKIs First commit after reorg Jun 11, 2013
lu_rnaseq Merged with master. Jul 11, 2013
lz_HSC_niche_effects/scripts final changes to script Apr 16, 2014
macklis_sox6_rnaseq Adding scripts for breault, macklis, teplyuk, and weiner consults Mar 22, 2016
mg_spikeins/scripts merging update Apr 27, 2015
mvm_functional_analysis/scripts add gprofiler analysis by direction of logFC Sep 12, 2016
na_ifrgamma_ko/scripts fix logfc filter and compare to past results Oct 6, 2016
na_vaccinia_scar/scripts batch exploration and correction Nov 22, 2016
pgen_23andme Improve readme with background and add explicit license Dec 11, 2013
pk_functional_gwas/scripts Update heatmaps.Rmd Mar 23, 2016
pk_gwaseq Added the filtering sugggestions script. Jul 6, 2012
rk_thesis Merged with master. Jul 11, 2013
rrbs_workflows/scripts First commit after reorg Jun 11, 2013
rs_knockout_array_analysis/scripts Update process.r Jan 22, 2014
rs_open_vs_closed_chromatin_analysis/scripts First commit after reorg Jun 11, 2013
sahay_klf9_overexpression_rnaseq Update before meeting Feb 23, 2017
sc_interneuron_microarray/scripts added new datasets Nov 16, 2016
scde_deploy Generalize to have BII only deployment target; reuse cloudbiolinux fu… Sep 6, 2011
seidman_rnaseq/scripts add in a few old scripts Dec 8, 2015
shi_wgbs/scripts regressions for hydroxymeth Sep 12, 2016
slack_lin28_rnaseq Adding scripts for henske analyses and slack analysis to github Oct 13, 2016
slim_rnaseq Mass update of legacy information from previous projects. Jun 3, 2013
snp-assess Provide java main class to enable easier access to snp-assess functio… Nov 26, 2013
stankovic_mirna2 adding report markdowns for all my completed/nearly completed consults Sep 17, 2015
sw_cardiomyocyte_differentiation First commit after reorg Jun 11, 2013
tanzi_ad Filtering of variants as input to downstream statistical analyses Jun 23, 2015
teplyuk_mir10b_align Adding scripts for breault, macklis, teplyuk, and weiner consults Mar 22, 2016
tp_shrna Support non-replicate differential expression analysis; generalize su… Nov 28, 2011
umemori_rnaseq adding report markdowns for all my completed/nearly completed consults Sep 17, 2015
vafai_ndufs4_rnaseq Added all complete markdowns for the vafai analysis May 25, 2016
vardict Snakemake script for VarDict complex indel comparison Jan 29, 2016
vs_ripchip/scripts add kusek kiebler overlap GO analyses Jan 5, 2017
vv_miRNA-Seq vishal functional analyses Jul 21, 2014
vv_smoc2KO_rnaseq/scripts final changes Jul 7, 2016
weiner_tcells_rnaseq Adding scripts for breault, macklis, teplyuk, and weiner consults Mar 22, 2016
wen_hiv Example for capture-recapture calculation added. Nov 19, 2013
widenmaier_rnaseq/scripts Added missing ggplot2 import. Feb 10, 2014
wp_rna_seq/scripts First commit after reorg Jun 11, 2013
zon_rnaseq Mass update of legacy information from previous projects. Jun 3, 2013
.gitignore RStudio default Feb 23, 2017
README.md Initial repository for HBC projects Mar 3, 2011

README.md

Various in-progress projects at Harvard School of Public Health Bioinformatics core