updating core functions and comments

getActivities corrected

standardize option and computing lambda max on a single core for large N…

swissregulon scan in TEs

swissregulon tss clustered

swissregulon scan of tss clusters, protein coding genes

swissregulon scan of TE in windows

producing results dir

local scratch path

correcting download of ucsc binaries

local analysis

analysis performed on the local machine

update

Merge branch 'master' of ssh://c4science.ch/diffusion/10523/tfbs_annotate_fimo

annotating hg19 promoters with ambrosini best4gene

fixed typo

not scaling E anymore (fix)

estimateRMSE

updated results of getSignifAct

removed the whole summary from the result of getSignifActivities.R

started new sample string

treatment and control groups added to the ouptut of getSignifActivities

added gc() to free memory during preprocess_E_N

corrected index bug for N_concat

added getSignifActivities.R

column centering E before row-centering

correcting broadcasting error in get_pseudocounts

giving N, plotting log tpm

preprocessing of E and N automatic

row_center.R

get_pseudocounts.R

getActivities with single lambda value across samples

do not correct names of predictors

typos

removing goldenpath link causing crash

tyding up get_tpm.R

tydied up get_tpm.R

get_tpm in separate file

typo

getActivities log ID

ylim on plotActivities

annotating hg19 promoters with ambrosini best4gene

added header to result file

concatenate and sort using unix sort instead of pandas

MEME format background model for 0-order, taking both strands into account

compute background frequencies

download faCount with script

data + notebook, cerebroviz

problem set 3 finished

writing output to file directly in each process (speed), subprocess.run instead…

removed matched sequences from output

pool instead of threadpool, using text output to standard output to avoid huge…

added input argv where necessary, still not optimal. Launched the analysis on…

working script for simple run_fimo

moved temp to scratch, run fimo on toy example, without scheduler

extract fasta

.gitignore corected*

gitignore, split bed file

download reference genome script

twoBitToFa

added README

problem set 3

problem set 2 exo 6

detected an anomaly for a ZKSCAN1 motif, removed the motif from the set to…

filtered out Transfac, non human, not directly determined motifs

MEME prototype converted matrix worked (with sanity checks)

prototype conversion from cisbp to meme, untested

6b think

initial commit

size of labels plotActivities

cvsd rename in res list

cvsd fix indexing problem

added cv error and cv std to the result lists of getActivities

added lamba_min to the return of getActivities

camelCap getActivities

corrected perspectives

plotActivities

TPM mappable normalization not finished

simple parallel with 1 core per glmnet instance, no parallel on CV

default k fold = 5

clean output as list of r2 and activities for get_activities

get_coefficients polished and tested on sample matrices. Not confirmed on whole…

get_coefficients for ISMARA like TF activity analysis, doesnt run yet

corrected high leverage function to work with hat and not hatvalues (predictor…

bullshit function purge high leverage points and aliases lm()

get aliased predictors from lm()

fixed conflict caused by --amend after push for high leverage points

high leverage points

high leverage points

R function source file get_TPM and correlation heatmap