Showing : diffHic • reset
2
votes
2
replies
103
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
17 days ago • updated 16 days ago nelsonmo • 0
0
votes
2
replies
136
views
Can't normalize samples in diffHic
diffHic
19 days ago • updated 14 days ago arielpaulson ▴ 20
1
vote
7
replies
403
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 11 months ago by ★ 27k • written 11 months ago by ▴ 30
0
votes
1
reply
142
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 15 months ago by ★ 27k • written 15 months ago by • 0
0
votes
1
reply
161
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 22 months ago by ★ 27k • written 22 months ago by • 0
0
votes
1
reply
212
views
conda install of diffHic
diffHic conda
updated 23 months ago by ★ 27k • written 23 months ago by • 0
1
vote
7
replies
436
views
Error while running normOffsets in diffhic
diffhic csaw
updated 24 months ago by ★ 27k • written 24 months ago by • 0
1
vote
2
replies
254
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 2.0 years ago by ★ 27k • written 2.0 years ago by • 0
0
votes
3
replies
314
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 2.0 years ago by ★ 27k • written 2.0 years ago by • 0
2
votes
3
replies
366
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
2.0 years ago shopnil99 • 0
0
votes
2
replies
298
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 2.3 years ago by ★ 27k • written 2.3 years ago by ▴ 10
0
votes
9
replies
460
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 2.6 years ago by ★ 27k • written 2.6 years ago by • 0
0
votes
1
reply
308
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
2.7 years ago • updated 2.6 years ago mictadlo • 0
0
votes
2
replies
284
views
Pre-processing for diffHiC
diffHiC
updated 2.8 years ago by ★ 27k • written 2.8 years ago by 57k
1
vote
1
reply
366
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 2.9 years ago by ★ 27k • written 2.9 years ago by • 0
0
votes
3
replies
2.8k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 3.7 years ago by • 0 • written 5.7 years ago by • 0
2
votes
1
reply
484
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 3.7 years ago by ★ 27k • written 3.7 years ago by ▴ 20
0
votes
3
replies
593
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 3.8 years ago by 25k • written 3.8 years ago by • 0
0
votes
8
replies
637
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 3.8 years ago by ★ 27k • written 3.8 years ago by ▴ 20
0
votes
10
replies
893
views
error running presplit_map.py
diffHic
3.8 years ago Eichan • 0
2
votes
2
replies
726
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
4.0 years ago sergio.espeso-gil • 0
2
votes
2
replies
1.2k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
4.1 years ago • updated 4.0 years ago e.jacobson • 0
0
votes
1
reply
407
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 4.2 years ago by ★ 27k • written 4.2 years ago by • 0
0
votes
6
replies
676
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 4.3 years ago by ★ 27k • written 4.3 years ago by ▴ 20
2
votes
1
reply
728
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 4.3 years ago by ★ 27k • written 4.3 years ago by ▴ 20
0
votes
1
reply
599
views
diffHic count data
diffhic
updated 4.5 years ago by ★ 27k • written 4.5 years ago by ▴ 10
2
votes
7
replies
652
views
diffHic: minimum counts per bin
diffhic edger
4.6 years ago andreucat91 • 0
5
votes
12
replies
1.6k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
4.6 years ago Sameet Mehta ▴ 30
1
vote
2
replies
542
views
Removing trended biases between HiC libraries
diffhic
updated 4.7 years ago by ★ 27k • written 4.7 years ago by ▴ 120
1
vote
3
replies
585
views
Interpreting strand orientation plots in diffHic
diffhic
updated 4.7 years ago by ★ 27k • written 4.7 years ago by ▴ 120
1
vote
4
replies
784
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 4.8 years ago by 57k • written 4.8 years ago by • 0
0
votes
3
replies
549
views
Error in plotDI in pacakge diffHic
diffHic plotDI
4.9 years ago Andrew • 0
0
votes
1
reply
594
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 4.9 years ago by ★ 27k • written 4.9 years ago by • 0
1
vote
4
replies
643
views
diffHic:Fails to load bam file during preparePairs
diffhic
4.9 years ago manjulathimma • 0
0
votes
2
replies
515
views
generate ContactMatrix from InteractionSet object
diffhic
4.9 years ago kamal.fartiyal84 ▴ 10
1
vote
3
replies
703
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 4.9 years ago by • 0 • written 4.9 years ago by • 0
1
vote
5
replies
728
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
5.0 years ago Vivek.b ▴ 100
0
votes
3
replies
640
views
diffHic: alternative input?
diffhic
5.0 years ago chiara.a.nicoletti • 0
0
votes
1
reply
569
views
diffHic preparePairs function
diffHic
updated 5.0 years ago by ★ 27k • written 5.0 years ago by • 0
0
votes
1
reply
511
views
diffHiC: Error when call preparePairs
diffhic
updated 5.1 years ago by ★ 27k • written 5.1 years ago by • 0
0
votes
1
reply
475
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 5.1 years ago by ★ 27k • written 5.1 years ago by • 0
0
votes
1
reply
452
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 20
1
vote
3
replies
540
views
diffHiC preparePairs error
diffhic preparepairs
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 20
0
votes
1
reply
567
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 5.2 years ago by ★ 27k • written 5.2 years ago by • 0
0
votes
1
reply
904
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 120
0
votes
5
replies
997
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 5.5 years ago by ★ 27k • written 5.5 years ago by • 0
0
votes
1
reply
761
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 5.7 years ago by ★ 27k • written 5.7 years ago by • 0
0
votes
1
reply
624
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 5.7 years ago by ★ 27k • written 5.7 years ago by • 0
1
vote
3
replies
775
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
5.7 years ago roladali ▴ 20
0
votes
6
replies
920
views
diffHic preparepairs issue
diffhic
5.8 years ago fine418 • 0
50 results • Page 1 of 1
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Comment: featureCounts - paired-end data by Yanfang • 0
Hey Wei shi, May I ask you something related to featureCounts? I have only paired end reads (RNAseq) mapping to its genome by bowtie2, an…
Comment: WGCNA adjust p value by Kevin Blighe 3.2k
Cross-posted: https://www.biostars.org/p/9482927/
Comment: Unique GPos taking into account mcols by Marcel Ramos 540
Hi @maltethodberg We currently do not have a method that does this. Perhaps a `duplicated` method is appropriate but I am not the develop…
Comment: What are these genes ? [How to get Ensembl IDs for them] by abf ▴ 30
Mouse genes are not typically all capitals, but I was able to find a reference to a mouse gene in NCBI to [CH36-217G15][1]. Maybe this is …
Comment: Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db. by abf ▴ 30
I should note that when I query org.Mm.eg.db using the gene Symbols associated with my differential expression data I find a 1:1 correspond…
Votes
A: Normalized counts of DESeq2 affected by design formula?
A: Finding orthologous human/mouse ENSEMBL IDs
Comment: What are these genes ? [How to get Ensembl IDs for them]
Answer: What lfcSE is dependent upon?
Comment: P value and Adj. P value showing N/A
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