Showing : diffhic • reset
2
votes
2
replies
718
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
2.4 years ago nelsonmo • 0
0
votes
2
replies
687
views
Can't normalize samples in diffHic
diffHic
2.4 years ago arielpaulson ▴ 20
1
vote
7
replies
1.4k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 30
0
votes
1
reply
690
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 3.6 years ago by ★ 28k • written 3.6 years ago by • 0
0
votes
1
reply
510
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 4.2 years ago by ★ 28k • written 4.2 years ago by • 0
0
votes
1
reply
904
views
conda install of diffHic
diffHic conda
updated 4.3 years ago by ★ 28k • written 4.3 years ago by • 0
1
vote
7
replies
1.4k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 4.3 years ago by ★ 28k • written 4.3 years ago by • 0
1
vote
2
replies
757
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
0
votes
3
replies
836
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 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
2
votes
3
replies
862
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
4.4 years ago shopnil99 • 0
0
votes
2
replies
757
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 10
0
votes
9
replies
1.2k
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
0
votes
1
reply
781
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
5.0 years ago mictadlo ▴ 10
0
votes
2
replies
606
views
Pre-processing for diffHiC
diffHiC
updated 5.1 years ago by ★ 28k • written 5.1 years ago by 64k
1
vote
1
reply
1.1k
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
0
votes
3
replies
4.0k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 6.0 years ago by • 0 • written 8.1 years ago by • 0
2
votes
1
reply
1.0k
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 20
0
votes
3
replies
1.1k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
0
votes
8
replies
1.3k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 20
0
votes
10
replies
1.7k
views
error running presplit_map.py
diffHic
6.1 years ago Eichan • 0
2
votes
2
replies
1.3k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
6.3 years ago sergio.espeso-gil • 0
2
votes
2
replies
2.2k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
6.4 years ago e.jacobson • 0
0
votes
1
reply
636
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
0
votes
6
replies
1.2k
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
2
votes
1
reply
1.1k
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 20
0
votes
1
reply
897
views
diffHic count data
diffhic
updated 6.8 years ago by ★ 28k • written 6.8 years ago by ▴ 10
2
votes
7
replies
1.1k
views
diffHic: minimum counts per bin
diffhic edger
7.0 years ago andreucat91 • 0
5
votes
12
replies
2.6k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
7.0 years ago Sameet Mehta ▴ 30
1
vote
2
replies
835
views
Removing trended biases between HiC libraries
diffhic
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 120
1
vote
3
replies
970
views
Interpreting strand orientation plots in diffHic
diffhic
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 120
1
vote
4
replies
1.2k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 7.1 years ago by 64k • written 7.1 years ago by • 0
0
votes
3
replies
802
views
Error in plotDI in pacakge diffHic
diffHic plotDI
7.2 years ago Andrew • 0
0
votes
1
reply
940
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
1
vote
4
replies
977
views
diffHic:Fails to load bam file during preparePairs
diffhic
7.3 years ago • updated 7.2 years ago manjulathimma • 0
0
votes
2
replies
881
views
generate ContactMatrix from InteractionSet object
diffhic
7.2 years ago kamal.fartiyal84 ▴ 10
1
vote
3
replies
1.2k
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 7.3 years ago by • 0 • written 7.3 years ago by • 0
1
vote
5
replies
1.2k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
7.3 years ago Vivek.b ▴ 100
0
votes
3
replies
1.0k
views
diffHic: alternative input?
diffhic
7.4 years ago • updated 7.3 years ago chiara.a.nicoletti • 0
0
votes
1
reply
905
views
diffHic preparePairs function
diffHic
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
0
votes
1
reply
784
views
diffHiC: Error when call preparePairs
diffhic
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
0
votes
1
reply
783
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
0
votes
1
reply
703
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 20
1
vote
3
replies
938
views
diffHiC preparePairs error
diffhic preparepairs
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 20
0
votes
1
reply
825
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
1
vote
1
reply
1.4k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 120
0
votes
5
replies
1.5k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
1
reply
983
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
0
votes
1
reply
927
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
1
vote
3
replies
1.1k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
8.1 years ago • updated 8.0 years ago roladali ▴ 20
0
votes
6
replies
1.5k
views
diffHic preparepairs issue
diffhic
8.2 years ago fine418 • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: GOslim missing GO term by amanda • 0
Thank you for the advice and many thanks! It is WGCNA analysis. I will try your method today and see if there are some consistencies.
Comment: GOslim missing GO term by James W. MacDonald 64k
Is this a WGCNA analysis (multiple co-expression clusters sounds like WGCNA)? If so, none of that is inferential or easily interpreted. It …
Comment: GOslim missing GO term by amanda • 0
For each group, I generated multiple co-expression clusters, and within each cluster, cluster PC1 was correlated with PC1 of multiple clini…
Comment: GOslim missing GO term by James W. MacDonald 64k
What do you mean by 'enriched with ... GO terms from their correlations with clinical traits'? Are you doing a GO hypergeometric or somethi…
Comment: GOslim missing GO term by amanda • 0
I have multiple groups to compare with, and each enriched with hundreds of GO terms from their correlations with clinical traits (top1 pval…
Votes
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
Awards • All
Scholar to James W. MacDonald 64k
Scholar to Assa Yeroslaviz ★ 1.5k
Popular Question to Gordon Smyth 48k
Popular Question to Endre Sebestyén ▴ 70
Popular Question to ramonfallon ▴ 20
Locations • All
Thailand, 36 minutes ago
United States, 43 minutes ago
Austria, 47 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
United Kingdom, 1 hour ago
Traffic: 415 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6