Publications by Sergio Garcia-Moreno Alcantara (
TFIID at promoter types (dmso)
Aim The aim of this analysis is to compare TFIID organization between TATA and DPE promoters using the half life data set. Enviroment setup #Standard packages library(rtracklayer); library(GenomicRanges); library(magrittr) ; library(Biostrings); library(BSgenome.Dmelanogaster.UCSC.dm6); library(multiClust) library(Hmisc); library(ggplot2) ; lib...
2477 sym R (22648 sym/19 pcs) 5 img
SAGA at promoter types
Aim The aim of this analysis is to compare the occupancy of the SAGA complex at different promoter types. Enviroment setup #Set working directory setwd("/n/projects/sga/analysis/SAGA/") #Standard packages library(rtracklayer); library(GenomicRanges); library(magrittr) ; library(Biostrings); library(BSgenome.Dmelanogaster.UCSC.dm6); library(mu...
1212 sym R (17496 sym/17 pcs) 4 img
TFIID at promoter types (triptolide)
Aim The aim of this analysis is to compare TFIID organization between TATA and DPE promoters using the half life data set. Enviroment setup #Standard packages library(rtracklayer); library(GenomicRanges); library(magrittr) ; library(Biostrings); library(BSgenome.Dmelanogaster.UCSC.dm6); library(multiClust) library(Hmisc); library(ggplot2) ; lib...
2477 sym R (22727 sym/19 pcs) 5 img
TFIID at individual promoters
Aim The aim of this analysis is look at TFIID occupancy at individual promoter types using promoter sets with a more stringent positioning of the motifs with respect to the TSS. Enviroment setup Set working directory and load required libraries and lab functions setwd("/n/projects/sga/analysis/tfiid/scripts/individual_promoters/") options(knitr....
3337 sym R (22836 sym/42 pcs) 38 img
dSMF
Aim To pre-process, align and analyze data from genome-wide double-enzyme single-molecule methylation footprinting (dSMF). Data from Dirk Schuebeler’s paper (2017). This analysis is performed using dm3 genome version as alignment to dm6 has been reported to have issues. Computational Setup wd <- "/n/projects/sga/analysis/dSMF/" setwd(wd) pack...
2533 sym R (19265 sym/20 pcs) 5 img
dSMF
Aim To pre-process, align and analyze data from genome-wide double-enzyme single-molecule methylation footprinting (dSMF). Data from Dirk Schuebeler’s paper (2017). This analysis is performed using dm3 genome version as alignment to dm6 has been reported to have issues. Computational Setup wd <- "/n/projects/sga/analysis/dSMF/" setwd(wd) pack...
2456 sym R (19649 sym/21 pcs) 7 img
Document
#Introduction Environment Setup Set working directory and load required libraries and lab functions setwd("/n/projects/sga/analysis/tfiid/scripts/tfiid_high_signal_metapeaks/") options(knitr.figure_dir = "plots/") #Standard packages library(rtracklayer); library(GenomicRanges); library(magrittr) ; library(Biostrings); library(reshape2); library...
493 sym R (11452 sym/21 pcs) 15 img
Motif enrichment at patterning enhancers (Kaelan)
1. Introduction Here, I will take the previously generated list of patterning enhancers and look at motif enrichment in these different classes of enhancers. 2. Computational Setup #Standard packages library(rtracklayer) ; library(GenomicRanges); library(magrittr) ; library(Biostrings) library(ggplot2) ; library(reshape2); library(plyranges); l...
2125 sym R (24715 sym/14 pcs) 5 img
TRF2 at cyclin genes - collaboration with Tamar Juven-Gershon lab
Aim Based on data from the lab Tamar Juven-Gershon, upon TRF2 knockdown in S2 cells, the levels of Cyclin A, B, B3 and E are reduced, but Cyclin C and D are not. The aim of this analysis is to look at TRF2 occupancy at the core promoter region of the genes Cyclin A, B, B3, E, C and D to test if there is any difference in occupancy at these genes....
1079 sym R (11763 sym/11 pcs) 7 img
Document
Aim Analysis of SAGA occupancy at active core promoters in the Drosophila ovaries Enviroment setup Set working directory and load required libraries and lab functions setwd("/n/projects/sga/analysis/SAGA/publication/") options(knitr.figure_dir = "plots/figure_4") #Standard packages library(GenomicAlignments); library(GenomicRanges); library(Bio...
732 sym R (16382 sym/9 pcs) 5 img