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Showing :
diffHic
•
reset
2
votes
2
replies
912
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
3.0 years ago
nelsonmo
• 0
0
votes
2
replies
844
views
Can't normalize samples in diffHic
diffHic
3.0 years ago
arielpaulson
▴ 20
1
vote
7
replies
1.7k
views
problem recasting InteractionSet into a DGEList
diffHic
GenomicInteractions
edgeR
HiC
cooler
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
Marco Blanchette
▴ 30
0
votes
1
reply
880
views
How to load counts from existing count matrices in diffHic package
diffHic
HiC
InteractionSet
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
girardot
• 0
0
votes
1
reply
676
views
diffHiC error in mergePairs.
diffHiC
rdhf5
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
kaivalya.shevade
• 0
0
votes
1
reply
1.1k
views
conda install of diffHic
diffHic
conda
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
smithgr
• 0
1
vote
7
replies
1.7k
views
Error while running normOffsets in diffhic
diffhic
csaw
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
shopnil99
• 0
1
vote
2
replies
917
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic
rotPlaid
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
shopnil99
• 0
0
votes
3
replies
1.1k
views
diffHic presplit_map.py --sig option for HiC libraries prepared with restriction enzyme cocktail from Arima genomics
diffhic
Arima Genomics
presplit_map.py
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
shopnil99
• 0
2
votes
3
replies
1.1k
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic
pysam.SamtoolsError
pysam.sort
5.0 years ago
shopnil99
• 0
0
votes
2
replies
969
views
diffHic ICE normalization PCA with NAs
diffHic
normalization
pca
NAs
HI-C
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
inzirio
▴ 10
0
votes
9
replies
1.5k
views
from denove contig assembly to chromosome bins
diffhic
gothic
hicup
hic-c
hic
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
mictadlo
▴ 10
0
votes
1
reply
939
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic
diffhic
gothic
hicup
hic-c
5.6 years ago
mictadlo
▴ 10
0
votes
2
replies
774
views
Pre-processing for diffHiC
diffHiC
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
James W. MacDonald
66k
1
vote
1
reply
1.4k
views
extract HiC contacts for a given BEDPE set of coordinates
hic
diffhic
chromatin
bedpe
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
gryderart
• 0
0
votes
3
replies
4.3k
views
Error while processing BAM file with Picard FixMateInformation
diffHic
diffhic
updated 6.6 years ago by
geryk.jan
• 0 • written 8.7 years ago by
koustav.pal
• 0
2
votes
1
reply
1.3k
views
Inflating interactionSets into a contact matrix
diffhic
hic
interactionset
contactmatrix
inflate
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
hwick1
▴ 20
0
votes
3
replies
1.3k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic
csaw
Rhtslib
updated 6.7 years ago by
Martin Morgan
25k • written 6.7 years ago by
favorov
• 0
0
votes
8
replies
1.7k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic
hic
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
hwick1
▴ 20
0
votes
10
replies
2.0k
views
error running presplit_map.py
diffHic
6.7 years ago
Eichan
• 0
2
votes
2
replies
1.5k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic
hicpro
hic
6.9 years ago
sergio.espeso-gil
• 0
3
votes
2
replies
2.4k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup
hi-c
diffhic
homer
7.0 years ago
e.jacobson
▴ 10
0
votes
1
reply
732
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
516356412
• 0
0
votes
6
replies
1.4k
views
min enrichment in peak calling with diffHiC?
diffhic
peak
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
hwick1
▴ 20
2
votes
1
reply
1.2k
views
diffHiC with no biological replicates?
diffhic
estimate dispersion value
glm
no replicates
deseq
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
hwick1
▴ 20
0
votes
1
reply
1000
views
diffHic count data
diffhic
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
kamal.fartiyal84
▴ 10
2
votes
7
replies
1.3k
views
diffHic: minimum counts per bin
diffhic
edger
7.6 years ago
andreucat91
• 0
5
votes
12
replies
3.0k
views
How to use diffHiC with existing contact matrices?
diffHiC
HiCPro
diffhic
7.6 years ago
Sameet Mehta
▴ 30
1
vote
2
replies
957
views
Removing trended biases between HiC libraries
diffhic
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
Darya Vanichkina
▴ 130
1
vote
3
replies
1.1k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
Darya Vanichkina
▴ 130
1
vote
4
replies
1.4k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 7.7 years ago by
James W. MacDonald
66k • written 7.7 years ago by
manjulathimma
• 0
0
votes
3
replies
923
views
Error in plotDI in pacakge diffHic
diffHic
plotDI
7.8 years ago
Andrew
• 0
0
votes
1
reply
1.1k
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid
diffHic
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
Andrew
• 0
1
vote
4
replies
1.1k
views
diffHic:Fails to load bam file during preparePairs
diffhic
7.8 years ago
manjulathimma
• 0
0
votes
2
replies
1.0k
views
generate ContactMatrix from InteractionSet object
diffhic
7.8 years ago
kamal.fartiyal84
▴ 10
1
vote
3
replies
1.4k
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 7.9 years ago by
tidecrepep
• 0 • written 7.9 years ago by
manjulathimma
• 0
1
vote
5
replies
1.4k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic
interactionset
7.9 years ago
Vivek.b
▴ 100
0
votes
3
replies
1.2k
views
diffHic: alternative input?
diffhic
8.0 years ago • updated 7.9 years ago
chiara.a.nicoletti
• 0
0
votes
1
reply
1.1k
views
diffHic preparePairs function
diffHic
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
lwtan90
• 0
0
votes
1
reply
899
views
diffHiC: Error when call preparePairs
diffhic
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
tolemac
• 0
0
votes
1
reply
895
views
diffHiC statistical test to check differences between conditions
diffHiC
statistical test
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
lazaris
• 0
0
votes
1
reply
807
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
roladali
▴ 20
1
vote
3
replies
1.1k
views
diffHiC preparePairs error
diffhic
preparepairs
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
roladali
▴ 20
0
votes
1
reply
942
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
wliao
• 0
1
vote
1
reply
1.6k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
Darya Vanichkina
▴ 130
1
vote
5
replies
1.8k
views
diffHic preparePairs() does not identify paired-end reads
diffHic
preparePairs
paired
BAM
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
ilyco
• 0
0
votes
1
reply
1.1k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 years ago by
rulicosentino
• 0
0
votes
1
reply
1.0k
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic
GRanges
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 years ago by
rulicosentino
• 0
1
vote
3
replies
1.2k
views
saving raw interaction matrices using diffHic
diffhic
interaction matrix
8.6 years ago
roladali
▴ 20
0
votes
6
replies
1.7k
views
diffHic preparepairs issue
diffhic
8.8 years ago
fine418
• 0
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Comment: limma comparison for small sample size and how to get covariance matrix
by
Gordon Smyth
51k
Your MDS plot is better than before, but you are still not following the recommendation for making for making such plots given in the limma…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Also, ``` > result <- mapUniProt( from = "EMBL-GenBank-DDBJ_CDS", to = "UniProtKB", query = c("ACF95883.1") ) > result From…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Ugh, here's the link https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Cre…
Answer: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.
Answer: XCMS2 of orbitrap data
by
Elodie
• 0
Hi, I have the same question, I have acquired MS2 data with PRM analysis and inclusion lists of several ions. I have a list of product ion…
Votes
Answer: EPIC array hg38 annotation?
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
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