Showing : diffHiC • reset
2
votes
2
replies
150
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
9 weeks ago • updated 8 weeks ago nelsonmo • 0
0
votes
2
replies
169
views
Can't normalize samples in diffHic
diffHic
9 weeks ago • updated 8 weeks ago arielpaulson ▴ 20
1
vote
7
replies
455
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 12 months ago by ★ 27k • written 12 months ago by ▴ 30
0
votes
1
reply
162
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 16 months ago by ★ 27k • written 16 months ago by • 0
0
votes
1
reply
182
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 24 months ago by ★ 27k • written 24 months ago by • 0
0
votes
1
reply
239
views
conda install of diffHic
diffHic conda
updated 2.1 years ago by ★ 27k • written 2.1 years ago by • 0
1
vote
7
replies
483
views
Error while running normOffsets in diffhic
diffhic csaw
updated 2.1 years ago by ★ 27k • written 2.1 years ago by • 0
1
vote
2
replies
279
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 2.1 years ago by ★ 27k • written 2.1 years ago by • 0
0
votes
3
replies
346
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 2.2 years ago by ★ 27k • written 2.2 years ago by • 0
2
votes
3
replies
406
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
2.2 years ago shopnil99 • 0
0
votes
2
replies
332
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 2.4 years ago by ★ 27k • written 2.4 years ago by ▴ 10
0
votes
9
replies
506
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 2.8 years ago by ★ 27k • written 2.8 years ago by • 0
0
votes
1
reply
326
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
2.8 years ago mictadlo • 0
0
votes
2
replies
304
views
Pre-processing for diffHiC
diffHiC
updated 2.9 years ago by ★ 27k • written 2.9 years ago by 58k
1
vote
1
reply
389
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 3.1 years ago by ★ 27k • written 3.1 years ago by • 0
0
votes
3
replies
2.8k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 3.8 years ago by • 0 • written 5.9 years ago by • 0
2
votes
1
reply
501
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 3.9 years ago by ★ 27k • written 3.9 years ago by ▴ 20
0
votes
3
replies
609
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 3.9 years ago by 25k • written 3.9 years ago by • 0
0
votes
8
replies
664
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 3.9 years ago by ★ 27k • written 3.9 years ago by ▴ 20
0
votes
10
replies
943
views
error running presplit_map.py
diffHic
3.9 years ago Eichan • 0
2
votes
2
replies
752
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
4.1 years ago sergio.espeso-gil • 0
2
votes
2
replies
1.3k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
4.2 years ago e.jacobson • 0
0
votes
1
reply
419
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 4.3 years ago by ★ 27k • written 4.3 years ago by • 0
0
votes
6
replies
702
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 4.4 years ago by ★ 27k • written 4.4 years ago by ▴ 20
2
votes
1
reply
743
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 4.5 years ago by ★ 27k • written 4.5 years ago by ▴ 20
0
votes
1
reply
611
views
diffHic count data
diffhic
updated 4.6 years ago by ★ 27k • written 4.6 years ago by ▴ 10
2
votes
7
replies
677
views
diffHic: minimum counts per bin
diffhic edger
4.8 years ago andreucat91 • 0
5
votes
12
replies
1.7k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
4.8 years ago Sameet Mehta ▴ 30
1
vote
2
replies
557
views
Removing trended biases between HiC libraries
diffhic
updated 4.8 years ago by ★ 27k • written 4.8 years ago by ▴ 120
1
vote
3
replies
604
views
Interpreting strand orientation plots in diffHic
diffhic
updated 4.8 years ago by ★ 27k • written 4.8 years ago by ▴ 120
1
vote
4
replies
848
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 4.9 years ago by 58k • written 4.9 years ago by • 0
0
votes
3
replies
560
views
Error in plotDI in pacakge diffHic
diffHic plotDI
5.0 years ago Andrew • 0
0
votes
1
reply
612
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 5.0 years ago by ★ 27k • written 5.0 years ago by • 0
1
vote
4
replies
663
views
diffHic:Fails to load bam file during preparePairs
diffhic
5.0 years ago manjulathimma • 0
0
votes
2
replies
535
views
generate ContactMatrix from InteractionSet object
diffhic
5.0 years ago kamal.fartiyal84 ▴ 10
1
vote
3
replies
722
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 5.1 years ago by • 0 • written 5.1 years ago by • 0
1
vote
5
replies
746
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
5.1 years ago Vivek.b ▴ 100
0
votes
3
replies
660
views
diffHic: alternative input?
diffhic
5.1 years ago chiara.a.nicoletti • 0
0
votes
1
reply
582
views
diffHic preparePairs function
diffHic
updated 5.2 years ago by ★ 27k • written 5.2 years ago by • 0
0
votes
1
reply
524
views
diffHiC: Error when call preparePairs
diffhic
updated 5.2 years ago by ★ 27k • written 5.2 years ago by • 0
0
votes
1
reply
491
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 5.2 years ago by ★ 27k • written 5.2 years ago by • 0
0
votes
1
reply
462
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 5.3 years ago by ★ 27k • written 5.3 years ago by ▴ 20
1
vote
3
replies
578
views
diffHiC preparePairs error
diffhic preparepairs
updated 5.3 years ago by ★ 27k • written 5.3 years ago by ▴ 20
0
votes
1
reply
576
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 5.3 years ago by ★ 27k • written 5.3 years ago by • 0
0
votes
1
reply
921
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 5.3 years ago by ★ 27k • written 5.3 years ago by ▴ 120
0
votes
5
replies
1.0k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 5.6 years ago by ★ 27k • written 5.6 years ago by • 0
0
votes
1
reply
773
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 5.8 years ago by ★ 27k • written 5.8 years ago by • 0
0
votes
1
reply
640
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 5.8 years ago by ★ 27k • written 5.8 years ago by • 0
1
vote
3
replies
795
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
5.8 years ago roladali ▴ 20
0
votes
6
replies
948
views
diffHic preparepairs issue
diffhic
6.0 years ago fine418 • 0
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Comment: Macbook M1 install genefilter failed by Alexandre • 0
Hi Michael, Sure > BiocManager::install("DESeq2") 'getOption("repos")' replaces Bioconductor standard repositories, see '?re…
Comment: Returning to edgeR version 3.26.1? by Mike Smith ★ 5.1k
I'll just advertise that anyone who wishes can check the changes by visiting https://code.bioconductor.org/browse/edgeR/commits/RELEASE_3_9…
Comment: Returning to edgeR version 3.26.1? by Gordon Smyth 43k
Dear James, We **absolutely** do not not make changes to edgeR results or syntax within a Bioconductor release. The only changes made to e…
Answer: Returning to edgeR version 3.26.1? by Gordon Smyth 43k
The only reason we make changes to packages is to improve them or to fix bugs, so I'm a bit dismayed that you're going back to a version of…
Comment: "ERROR: cannot create temp file" when using buildindex from Rsubread by Yang Liao ▴ 260
You can try this: touch test.txt ; ls -l test.txt But given that you have created two sub-directories under the current directory, …
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Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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