Files in rr1859/R.4Cker
Analysis of 4C-seq (circularized chromosome conformation capture) data
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R.4Cker.Rproj
R/buildAdaptiveWindowsCis.R
R/buildAdaptiveWindowsTrans.R
R/cisAnalysis.R
R/createR4CkerObject.R
R/differentialAnalysis.R
R/generateSyntheticSamples.R
R/getWindowCounts.R
R/merge_windows.R
R/nearBaitAnalysis.R
R/normalizeCounts.R
R/parameterEstimation.R
R/removePCR.R
R/startingValues.R
R/transAnalysis.R
R/validateParameters.R
R/viterbi3State.R
README.md
bedGraph_files/CD83_HindIII_1.bedGraph
bedGraph_files/CD83_HindIII_2.bedGraph
bedGraph_files/Dileep_Ch16B30_PM_2hrs_1.bedGraph
bedGraph_files/Dileep_Ch16B30_PM_2hrs_2.bedGraph
bedGraph_files/IghCg1_HindIII_1.bedGraph
bedGraph_files/IghCg1_HindIII_2.bedGraph
bedGraph_files/Igk_MiEk_DN_WT_1.bedGraph
bedGraph_files/Igk_MiEk_DN_WT_2.bedGraph
bedGraph_files/Igk_MiEk_ImmB_WT_1.bedGraph
bedGraph_files/Igk_MiEk_ImmB_WT_2.bedGraph
bedGraph_files/Marin_Mouse_six1_E14_1.bedGraph
bedGraph_files/Marin_Mouse_six1_E14_2.bedGraph
bedGraph_files/Marin_Mouse_six2_E14_1.bedGraph
bedGraph_files/Marin_Mouse_six2_E14_2.bedGraph
bedGraph_files/Tcrb_Eb_DN_WT_1.bedGraph
bedGraph_files/Tcrb_Eb_DN_WT_2.bedGraph
bedGraph_files/Tcrb_Eb_ImmB_WT_1.bedGraph
bedGraph_files/Tcrb_Eb_ImmB_WT_2.bedGraph
bedGraph_files/denholtz_mm_hind_dppa2_1.bedGraph
bedGraph_files/denholtz_mm_hind_dppa2_2.bedGraph
bedGraph_files/denholtz_mm_hind_dppa2_3.bedGraph
bedGraph_files/denholtz_mm_hind_pcdhb19_1.bedGraph
bedGraph_files/denholtz_mm_hind_pcdhb19_2.bedGraph
bedGraph_files/denholtz_mm_hind_pcdhb19_3.bedGraph
bedGraph_files/denholtz_mm_hind_pouf51_1.bedGraph
bedGraph_files/denholtz_mm_hind_pouf51_3.bedGraph
bedGraph_files/gao_mm_hind_pou5f1_1.bedGraph
bedGraph_files/gao_mm_hind_pou5f1_2.bedGraph
bedGraph_files/mm10_hindiii_flanking_sites_25_unique_2.bed.gz
bedGraph_files/varun_mm_dpn_hoxa10_1.bedGraph
bedGraph_files/varun_mm_dpn_hoxa10_2.bedGraph
bedGraph_files/varun_mm_dpn_hoxa10_3.bedGraph
bglii.fa
csp6i.fa
data/CD83_HindIII.rda
data/Denholtz_dppa2.rda
data/Denholtz_pcdhb19.rda
data/Denholtz_pou5f1.rda
data/Dileep_Ch16B30.rda
data/Gao_pou5f1.rda
data/Hoxa10.rda
data/Igh_HindIII.rda
data/Igk_MiEk_DN_ImmB_WT.rda
data/Marin_six1.rda
data/Marin_six2.rda
data/Tcrb_Eb_DN_ImmB_WT.rda
dpnii.fa
hindiii.fa
nlaiii.fa
reduced_genome.sh
sam_bedGraph.sh
