Showing : diffHic • reset
2
votes
2
replies
251
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
6 months ago nelsonmo • 0
0
votes
2
replies
231
views
Can't normalize samples in diffHic
diffHic
6 months ago arielpaulson ▴ 20
1
vote
7
replies
545
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 17 months ago by ★ 27k • written 17 months ago by ▴ 30
0
votes
1
reply
214
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 21 months ago by ★ 27k • written 21 months ago by • 0
0
votes
1
reply
222
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 2.3 years ago by ★ 27k • written 2.3 years ago by • 0
0
votes
1
reply
292
views
conda install of diffHic
diffHic conda
updated 2.4 years ago by ★ 27k • written 2.4 years ago by • 0
1
vote
7
replies
604
views
Error while running normOffsets in diffhic
diffhic csaw
updated 2.5 years ago by ★ 27k • written 2.5 years ago by • 0
1
vote
2
replies
342
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 2.5 years ago by ★ 27k • written 2.5 years ago by • 0
0
votes
3
replies
403
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 2.5 years ago by ★ 27k • written 2.5 years ago by • 0
2
votes
3
replies
462
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
2.5 years ago shopnil99 • 0
0
votes
2
replies
376
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 2.8 years ago by ★ 27k • written 2.8 years ago by ▴ 10
0
votes
9
replies
578
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 3.1 years ago by ★ 27k • written 3.1 years ago by • 0
0
votes
1
reply
374
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
3.1 years ago mictadlo • 0
0
votes
2
replies
338
views
Pre-processing for diffHiC
diffHiC
updated 3.2 years ago by ★ 27k • written 3.2 years ago by 58k
1
vote
1
reply
448
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 3.4 years ago by ★ 27k • written 3.4 years ago by • 0
0
votes
3
replies
3.1k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 4.2 years ago by • 0 • written 6.2 years ago by • 0
2
votes
1
reply
547
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 4.2 years ago by ★ 27k • written 4.2 years ago by ▴ 20
0
votes
3
replies
698
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 4.2 years ago by 25k • written 4.2 years ago by • 0
0
votes
8
replies
743
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 4.2 years ago by ★ 27k • written 4.2 years ago by ▴ 20
0
votes
10
replies
1.0k
views
error running presplit_map.py
diffHic
4.3 years ago • updated 4.2 years ago Eichan • 0
2
votes
2
replies
804
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
4.5 years ago sergio.espeso-gil • 0
2
votes
2
replies
1.5k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
4.6 years ago • updated 4.5 years ago e.jacobson • 0
0
votes
1
reply
444
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 4.6 years ago by ★ 27k • written 4.6 years ago by • 0
0
votes
6
replies
776
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 4.7 years ago by ★ 27k • written 4.7 years ago by ▴ 20
2
votes
1
reply
790
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 4.8 years ago by ★ 27k • written 4.8 years ago by ▴ 20
0
votes
1
reply
642
views
diffHic count data
diffhic
updated 5.0 years ago by ★ 27k • written 5.0 years ago by ▴ 10
2
votes
7
replies
715
views
diffHic: minimum counts per bin
diffhic edger
5.1 years ago andreucat91 • 0
5
votes
12
replies
1.8k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
5.1 years ago Sameet Mehta ▴ 30
1
vote
2
replies
586
views
Removing trended biases between HiC libraries
diffhic
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 120
1
vote
3
replies
661
views
Interpreting strand orientation plots in diffHic
diffhic
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 120
1
vote
4
replies
924
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 5.3 years ago by 58k • written 5.3 years ago by • 0
0
votes
3
replies
593
views
Error in plotDI in pacakge diffHic
diffHic plotDI
5.3 years ago Andrew • 0
0
votes
1
reply
658
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 5.3 years ago by ★ 27k • written 5.3 years ago by • 0
1
vote
4
replies
709
views
diffHic:Fails to load bam file during preparePairs
diffhic
5.4 years ago • updated 5.3 years ago manjulathimma • 0
0
votes
2
replies
573
views
generate ContactMatrix from InteractionSet object
diffhic
5.4 years ago kamal.fartiyal84 ▴ 10
1
vote
3
replies
760
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 5.4 years ago by • 0 • written 5.4 years ago by • 0
1
vote
5
replies
788
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
5.5 years ago Vivek.b ▴ 100
0
votes
3
replies
706
views
diffHic: alternative input?
diffhic
5.5 years ago chiara.a.nicoletti • 0
0
votes
1
reply
612
views
diffHic preparePairs function
diffHic
updated 5.5 years ago by ★ 27k • written 5.5 years ago by • 0
0
votes
1
reply
560
views
diffHiC: Error when call preparePairs
diffhic
updated 5.5 years ago by ★ 27k • written 5.5 years ago by • 0
0
votes
1
reply
528
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 5.6 years ago by ★ 27k • written 5.6 years ago by • 0
0
votes
1
reply
494
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 5.6 years ago by ★ 27k • written 5.6 years ago by ▴ 20
1
vote
3
replies
615
views
diffHiC preparePairs error
diffhic preparepairs
updated 5.6 years ago by ★ 27k • written 5.6 years ago by ▴ 20
0
votes
1
reply
602
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 5.7 years ago by ★ 27k • written 5.7 years ago by • 0
0
votes
1
reply
975
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 5.7 years ago by ★ 27k • written 5.7 years ago by ▴ 120
0
votes
5
replies
1.1k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 5.9 years ago by ★ 27k • written 5.9 years ago by • 0
0
votes
1
reply
796
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 6.1 years ago by ★ 27k • written 6.1 years ago by • 0
0
votes
1
reply
668
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 6.2 years ago by ★ 27k • written 6.2 years ago by • 0
1
vote
3
replies
830
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
6.2 years ago roladali ▴ 20
0
votes
6
replies
1.1k
views
diffHic preparepairs issue
diffhic
6.3 years ago fine418 • 0
50 results • Page 1 of 1
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Comment: Trying to follow a gene set analyisis in R by Michael Love 35k
It looks like you only have a single sample.
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I get the following > design = model.matrix(~ es$condition) > design (Intercept) es$conditiondex4 attr(,"assign") [1] 0 1 attr(,"co…
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Annotation to the *subjunc* aligner helps the aligner to better map the reads. The aligner generates BAM files, which contains mapped reads…
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Hi, After doing some digging I've isolated the issue to being related to the threshold calculation which you request with the `threshold…
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Agree with swbarnes2. It just seems like the condition effect is very small. Also I'd double check the metadata. Sometimes samples are swap…
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