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In-progress projects at Harvard School of Public Health Bioinformaitcs Core
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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
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 17, 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 Collapse speedseq parallel regions into a smaller number of blocks Mar 26, 2016
gu_rnaseq trying to resolve directory structure differences Mar 23, 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 Update download to latest release Mar 21, 2013
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 dropping possible male samples May 11, 2016
kobzik_influenza Updating some older projects. Aug 24, 2013
kraft_wgs Added scripts used to annotate the genomes. Jun 3, 2013
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 reported version Dec 16, 2015
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
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 complete fdr analysis May 6, 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 25, 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
vardict Snakemake script for VarDict complex indel comparison Jan 29, 2016
vs_ripchip/scripts add GO enrichments May 10, 2016
vv_miRNA-Seq vishal functional analyses Jul 21, 2014
vv_smoc2KO_rnaseq/scripts DE and initial functional analysis May 24, 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 Snakemake script for VarDict complex indel comparison Jan 29, 2016
README.md Initial repository for HBC projects Mar 3, 2011

README.md

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

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