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pulver (Cyril David Son-Tuyen Pulver)

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User Details

User Since
Dec 5 2018, 10:29 (279 w, 6 d)
Availability
Available
Organization
epfl.ch (university)

Recent Activity

Oct 22 2021

pulver committed R10177:e0c09ada6d27: updating core functions and comments (authored by pulver).
updating core functions and comments
Oct 22 2021, 11:35

May 10 2021

pulver committed R10177:9e7f8f8ea37a: getActivities corrected (authored by pulver).
getActivities corrected
May 10 2021, 11:58
pulver committed R10177:41025990ec59: standardize option and computing lambda max on a single core for large N… (authored by pulver).
standardize option and computing lambda max on a single core for large N…
May 10 2021, 11:51

May 5 2021

pulver committed R10523:f61890f69f76: swissregulon scan in TEs (authored by pulver).
swissregulon scan in TEs
May 5 2021, 11:40

Apr 23 2021

pulver committed R10523:1ed5a91f7632: swissregulon tss clustered (authored by pulver).
swissregulon tss clustered
Apr 23 2021, 11:19

Apr 22 2021

pulver committed R10523:b8b8477cd08c: swissregulon scan of tss clusters, protein coding genes (authored by pulver).
swissregulon scan of tss clusters, protein coding genes
Apr 22 2021, 10:45

Apr 21 2021

pulver committed R10523:6019ae089167: swissregulon scan of TE in windows (authored by pulver).
swissregulon scan of TE in windows
Apr 21 2021, 14:35

Apr 12 2021

pulver committed R10523:0d8b7056863a: producing results dir (authored by pulver).
producing results dir
Apr 12 2021, 14:41
pulver committed R10523:4430ecaacffa: local scratch path (authored by pulver).
local scratch path
Apr 12 2021, 14:10
pulver committed R10523:ccac380801c4: correcting download of ucsc binaries (authored by pulver).
correcting download of ucsc binaries
Apr 12 2021, 13:58
pulver committed R10523:154a103238b8: local analysis (authored by pulver).
local analysis
Apr 12 2021, 13:48
pulver committed R10523:cf4612682d98: analysis performed on the local machine (authored by pulver).
analysis performed on the local machine
Apr 12 2021, 13:32

Apr 8 2021

pulver committed R10523:a1d993c0bab8: update (authored by pulver).
update
Apr 8 2021, 14:53
pulver committed R10523:415f55289e4d: Merge branch 'master' of ssh://c4science.ch/diffusion/10523/tfbs_annotate_fimo (authored by pulver).
Merge branch 'master' of ssh://c4science.ch/diffusion/10523/tfbs_annotate_fimo
Apr 8 2021, 14:53
pulver committed R10523:2e934c17f90b: annotating hg19 promoters with ambrosini best4gene (authored by pulver).
annotating hg19 promoters with ambrosini best4gene
Apr 8 2021, 14:53

Mar 24 2021

pulver committed R10177:8c6eedd021ee: fixed typo (authored by pulver).
fixed typo
Mar 24 2021, 13:00
pulver committed R10177:ddb95f8614d6: not scaling E anymore (fix) (authored by pulver).
not scaling E anymore (fix)
Mar 24 2021, 12:34

Mar 9 2021

pulver committed R10177:aa20a422d671: estimateRMSE (authored by pulver).
estimateRMSE
Mar 9 2021, 15:03

Mar 8 2021

pulver committed R10177:fb7910dfeaa3: updated results of getSignifAct (authored by pulver).
updated results of getSignifAct
Mar 8 2021, 14:47

Jan 5 2021

pulver committed R10177:6388e9e8b295: removed the whole summary from the result of getSignifActivities.R (authored by pulver).
removed the whole summary from the result of getSignifActivities.R
Jan 5 2021, 14:20

Jan 4 2021

pulver committed R10177:7faa6aa4bff3: started new sample string (authored by pulver).
started new sample string
Jan 4 2021, 12:07
pulver committed R10177:6b73088ced3f: treatment and control groups added to the ouptut of getSignifActivities (authored by pulver).
treatment and control groups added to the ouptut of getSignifActivities
Jan 4 2021, 10:19

Dec 16 2020

pulver committed R10177:45179506f662: added gc() to free memory during preprocess_E_N (authored by pulver).
added gc() to free memory during preprocess_E_N
Dec 16 2020, 16:40
pulver committed R10177:f2878aa0a65c: corrected index bug for N_concat (authored by pulver).
corrected index bug for N_concat
Dec 16 2020, 15:38

Dec 14 2020

pulver committed R10177:d1d772f30198: added getSignifActivities.R (authored by pulver).
added getSignifActivities.R
Dec 14 2020, 15:54
pulver committed R10177:f7db3c4ae278: column centering E before row-centering (authored by pulver).
column centering E before row-centering
Dec 14 2020, 12:54

Oct 5 2020

pulver committed R10177:bececb767f56: correcting broadcasting error in get_pseudocounts (authored by pulver).
correcting broadcasting error in get_pseudocounts
Oct 5 2020, 17:09

Oct 2 2020

pulver committed R10177:d4ff7541dee4: giving N, plotting log tpm (authored by pulver).
giving N, plotting log tpm
Oct 2 2020, 16:03
pulver committed R10177:3d8460088d95: preprocessing of E and N automatic (authored by pulver).
preprocessing of E and N automatic
Oct 2 2020, 15:43
pulver committed R10177:009fa13b09e5: row_center.R (authored by pulver).
row_center.R
Oct 2 2020, 14:51
pulver committed R10177:b2f5e5c3acba: get_pseudocounts.R (authored by pulver).
get_pseudocounts.R
Oct 2 2020, 14:50

Sep 28 2020

pulver committed R10177:3fc7a956c985: getActivities with single lambda value across samples (authored by pulver).
getActivities with single lambda value across samples
Sep 28 2020, 19:19

Sep 24 2020

pulver committed R10177:b0befcd88f65: do not correct names of predictors (authored by pulver).
do not correct names of predictors
Sep 24 2020, 14:47

Sep 16 2020

pulver committed R10177:a3ee0478f38a: typos (authored by pulver).
typos
Sep 16 2020, 14:38
pulver committed R10177:8aa38fb18466: removing goldenpath link causing crash (authored by pulver).
removing goldenpath link causing crash
Sep 16 2020, 14:38
pulver committed R10177:40a28e5bfd2c: tyding up get_tpm.R (authored by pulver).
tyding up get_tpm.R
Sep 16 2020, 14:09
pulver committed R10177:3ebba925f3ad: tydied up get_tpm.R (authored by pulver).
tydied up get_tpm.R
Sep 16 2020, 11:14
pulver committed R10177:49baf4cb6710: get_tpm in separate file (authored by pulver).
get_tpm in separate file
Sep 16 2020, 10:51

Sep 15 2020

pulver committed R10177:3f1e68b9bacd: typo (authored by pulver).
typo
Sep 15 2020, 14:35
pulver committed R10177:351a1bdc9336: getActivities log ID (authored by pulver).
getActivities log ID
Sep 15 2020, 13:36
pulver committed R10177:3f5290bdbc76: ylim on plotActivities (authored by pulver).
ylim on plotActivities
Sep 15 2020, 10:31

Aug 24 2020

pulver committed R10523:f8e666df22e7: annotating hg19 promoters with ambrosini best4gene (authored by pulver).
annotating hg19 promoters with ambrosini best4gene
Aug 24 2020, 09:57

Aug 19 2020

pulver committed R10523:5360dc02d451: added header to result file (authored by pulver).
added header to result file
Aug 19 2020, 17:35
pulver committed R10523:2e72ce521fd6: concatenate and sort using unix sort instead of pandas (authored by pulver).
concatenate and sort using unix sort instead of pandas
Aug 19 2020, 16:24
pulver committed R10523:b1adb46512f4: MEME format background model for 0-order, taking both strands into account (authored by pulver).
MEME format background model for 0-order, taking both strands into account
Aug 19 2020, 10:00

Aug 18 2020

pulver committed R10523:fe8cff74718a: compute background frequencies (authored by pulver).
compute background frequencies
Aug 18 2020, 18:19
pulver committed R10523:09191d77acf2: download faCount with script (authored by pulver).
download faCount with script
Aug 18 2020, 17:11

Jul 10 2020

pulver committed R10668:63bbb1f3ab6c: data + notebook, cerebroviz (authored by pulver).
data + notebook, cerebroviz
Jul 10 2020, 17:17

Jul 6 2020

pulver committed R10570:b332ea332263: problem set 3 finished (authored by pulver).
problem set 3 finished
Jul 6 2020, 15:19

Jul 1 2020

pulver committed R10523:c996bff49f9b: writing output to file directly in each process (speed), subprocess.run instead… (authored by pulver).
writing output to file directly in each process (speed), subprocess.run instead…
Jul 1 2020, 11:26
pulver committed R10523:473da4e5dc1f: removed matched sequences from output (authored by pulver).
removed matched sequences from output
Jul 1 2020, 11:26

Jun 30 2020

pulver committed R10523:b6d9ba449a47: pool instead of threadpool, using text output to standard output to avoid huge… (authored by pulver).
pool instead of threadpool, using text output to standard output to avoid huge…
Jun 30 2020, 18:51

Jun 29 2020

pulver committed R10523:54c09d669aae: added input argv where necessary, still not optimal. Launched the analysis on… (authored by pulver).
added input argv where necessary, still not optimal. Launched the analysis on…
Jun 29 2020, 19:13
pulver committed R10523:73d080087c1c: working script for simple run_fimo (authored by pulver).
working script for simple run_fimo
Jun 29 2020, 18:30
pulver committed R10523:8c9cdf69492d: moved temp to scratch, run fimo on toy example, without scheduler (authored by pulver).
moved temp to scratch, run fimo on toy example, without scheduler
Jun 29 2020, 17:00
pulver committed R10523:72b0aec13785: extract fasta (authored by pulver).
extract fasta
Jun 29 2020, 14:36
pulver committed R10523:77b57b518348: .gitignore corected* (authored by pulver).
.gitignore corected*
Jun 29 2020, 13:44
pulver committed R10523:49de628d2146: gitignore, split bed file (authored by pulver).
gitignore, split bed file
Jun 29 2020, 13:43

Jun 26 2020

pulver committed R10523:7ac2c32a2451: download reference genome script (authored by pulver).
download reference genome script
Jun 26 2020, 18:13
pulver committed R10523:cc02afdf5e57: twoBitToFa (authored by pulver).
twoBitToFa
Jun 26 2020, 18:13
pulver committed R10523:46708ffbfb05: added README (authored by pulver).
added README
Jun 26 2020, 11:55
pulver committed R10570:bfc12dd98b66: problem set 3 (authored by pulver).
problem set 3
Jun 26 2020, 10:23

Jun 24 2020

pulver committed R10570:db844712f77a: problem set 2 exo 6 (authored by pulver).
problem set 2 exo 6
Jun 24 2020, 17:55

Jun 16 2020

pulver committed R10595:070ad35043e1: detected an anomaly for a ZKSCAN1 motif, removed the motif from the set to… (authored by pulver).
detected an anomaly for a ZKSCAN1 motif, removed the motif from the set to…
Jun 16 2020, 18:23
pulver committed R10595:7b2a68bcab8f: filtered out Transfac, non human, not directly determined motifs (authored by pulver).
filtered out Transfac, non human, not directly determined motifs
Jun 16 2020, 18:23
pulver committed R10595:4f5248d3bebe: MEME prototype converted matrix worked (with sanity checks) (authored by pulver).
MEME prototype converted matrix worked (with sanity checks)
Jun 16 2020, 15:03
pulver committed R10595:ce52ce681f41: prototype conversion from cisbp to meme, untested (authored by pulver).
prototype conversion from cisbp to meme, untested
Jun 16 2020, 14:08

Jun 10 2020

pulver committed R10570:5bb8245f8019: 6b think (authored by pulver).
6b think
Jun 10 2020, 11:03

May 27 2020

pulver committed R10523:1f240e46a86e: initial commit (authored by pulver).
initial commit
May 27 2020, 12:40

Apr 22 2020

pulver committed R10177:1c05ceb60837: size of labels plotActivities (authored by pulver).
size of labels plotActivities
Apr 22 2020, 17:18

Apr 16 2020

pulver committed R10177:b3bb144caa65: cvsd rename in res list (authored by pulver).
cvsd rename in res list
Apr 16 2020, 13:39
pulver committed R10177:0df5e1dc3da4: cvsd fix indexing problem (authored by pulver).
cvsd fix indexing problem
Apr 16 2020, 13:37
pulver committed R10177:6893a2a12861: added cv error and cv std to the result lists of getActivities (authored by pulver).
added cv error and cv std to the result lists of getActivities
Apr 16 2020, 10:28
pulver committed R10177:2ef96af9c686: added lamba_min to the return of getActivities (authored by pulver).
added lamba_min to the return of getActivities
Apr 16 2020, 10:19

Apr 15 2020

pulver committed R10177:48057c61b909: camelCap getActivities (authored by pulver).
camelCap getActivities
Apr 15 2020, 15:31

Apr 9 2020

pulver committed R10177:1d8d54950a2f: corrected perspectives (authored by pulver).
corrected perspectives
Apr 9 2020, 19:48
pulver committed R10177:d4a2d7ac5a71: plotActivities (authored by pulver).
plotActivities
Apr 9 2020, 18:29
pulver committed R10177:c66180c8bfd1: TPM mappable normalization not finished (authored by pulver).
TPM mappable normalization not finished
Apr 9 2020, 09:47

Apr 6 2020

pulver committed R10177:5f9fd1c6fd93: simple parallel with 1 core per glmnet instance, no parallel on CV (authored by pulver).
simple parallel with 1 core per glmnet instance, no parallel on CV
Apr 6 2020, 19:34

Apr 3 2020

pulver committed R10177:f7804fe4fb09: default k fold = 5 (authored by pulver).
default k fold = 5
Apr 3 2020, 19:25
pulver committed R10177:cecfd2d4e51d: clean output as list of r2 and activities for get_activities (authored by pulver).
clean output as list of r2 and activities for get_activities
Apr 3 2020, 18:56

Mar 24 2020

pulver committed R10177:15c3143b1f5d: get_coefficients polished and tested on sample matrices. Not confirmed on whole… (authored by pulver).
get_coefficients polished and tested on sample matrices. Not confirmed on whole…
Mar 24 2020, 17:39

Mar 23 2020

pulver committed R10177:2c9dca0a3566: get_coefficients for ISMARA like TF activity analysis, doesnt run yet (authored by pulver).
get_coefficients for ISMARA like TF activity analysis, doesnt run yet
Mar 23 2020, 18:43

Mar 16 2020

pulver committed R10177:9c18b24957b9: corrected high leverage function to work with hat and not hatvalues (predictor… (authored by pulver).
corrected high leverage function to work with hat and not hatvalues (predictor…
Mar 16 2020, 19:26
pulver committed R10177:06f2b57d66dd: bullshit function purge high leverage points and aliases lm() (authored by pulver).
bullshit function purge high leverage points and aliases lm()
Mar 16 2020, 18:39
pulver committed R10177:998681712f0b: get aliased predictors from lm() (authored by pulver).
get aliased predictors from lm()
Mar 16 2020, 15:39
pulver committed R10177:30705d0969a7: fixed conflict caused by --amend after push for high leverage points (authored by pulver).
fixed conflict caused by --amend after push for high leverage points
Mar 16 2020, 10:39
pulver committed R10177:2210fb6c958f: high leverage points (authored by pulver).
high leverage points
Mar 16 2020, 10:39
pulver committed R10177:894d5020d0d8: high leverage points (authored by pulver).
high leverage points
Mar 16 2020, 10:02

Mar 11 2020

pulver committed R10177:fd2803c34f0a: R function source file get_TPM and correlation heatmap (authored by pulver).
R function source file get_TPM and correlation heatmap
Mar 11 2020, 09:19

Jan 15 2020

pulver set Organization to epfl.ch (university) on pulver.
Jan 15 2020, 11:07