Showing : diffHic • reset
2
votes
2
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891
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
2.9 years ago nelsonmo • 0
0
votes
2
replies
825
views
Can't normalize samples in diffHic
diffHic
2.9 years ago arielpaulson ▴ 20
1
vote
7
replies
1.6k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 30
0
votes
1
reply
871
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 4.1 years ago by ★ 28k • written 4.1 years ago by • 0
0
votes
1
reply
671
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
0
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1
reply
1.1k
views
conda install of diffHic
diffHic conda
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
vote
7
replies
1.7k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
1
vote
2
replies
905
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 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 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
2
votes
3
replies
1.0k
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
4.9 years ago shopnil99 • 0
0
votes
2
replies
941
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 10
0
votes
9
replies
1.5k
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 10
0
votes
1
reply
930
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
5.5 years ago mictadlo ▴ 10
0
votes
2
replies
766
views
Pre-processing for diffHiC
diffHiC
updated 5.6 years ago by ★ 28k • written 5.6 years ago by 66k
1
vote
1
reply
1.4k
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
0
votes
3
replies
4.3k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 6.6 years ago by • 0 • written 8.6 years ago by • 0
2
votes
1
reply
1.2k
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
0
votes
3
replies
1.3k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
0
votes
8
replies
1.6k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 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 • updated 6.9 years ago e.jacobson ▴ 10
0
votes
1
reply
727
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 7.0 years ago by ★ 28k • written 7.0 years ago by • 0
0
votes
6
replies
1.3k
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 20
2
votes
1
reply
1.2k
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 20
0
votes
1
reply
994
views
diffHic count data
diffhic
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 10
2
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7
replies
1.3k
views
diffHic: minimum counts per bin
diffhic edger
7.5 years ago andreucat91 • 0
5
votes
12
replies
3.0k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
7.5 years ago Sameet Mehta ▴ 30
1
vote
2
replies
951
views
Removing trended biases between HiC libraries
diffhic
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 130
1
vote
3
replies
1.1k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 130
1
vote
4
replies
1.3k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 7.7 years ago by 66k • written 7.7 years ago by • 0
0
votes
3
replies
917
views
Error in plotDI in pacakge diffHic
diffHic plotDI
7.7 years ago Andrew • 0
0
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1
reply
1.1k
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
1
vote
4
replies
1.1k
views
diffHic:Fails to load bam file during preparePairs
diffhic
7.8 years ago • updated 7.7 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 7.8 years ago by • 0 • written 7.8 years ago by • 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
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3
replies
1.2k
views
diffHic: alternative input?
diffhic
7.9 years ago chiara.a.nicoletti • 0
0
votes
1
reply
1.1k
views
diffHic preparePairs function
diffHic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
1
reply
894
views
diffHiC: Error when call preparePairs
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
1
reply
890
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
0
votes
1
reply
798
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 20
1
vote
3
replies
1.1k
views
diffHiC preparePairs error
diffhic preparepairs
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 20
0
votes
1
reply
935
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 8.1 years ago by ★ 28k • written 8.1 years ago by • 0
1
vote
1
reply
1.5k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 130
1
vote
5
replies
1.8k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 8.3 years ago by ★ 28k • written 8.3 years ago by • 0
0
votes
1
reply
1.1k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 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 ★ 28k • written 8.6 years ago by • 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
8.7 years ago fine418 • 0
50 results • Page 1 of 1
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Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
Well, I was looking at the result table (enrich18k@result, or yy@result in your example), and it gives every pathway even the non-significa…
Comment: Trouble reading samplesheet in with diffbind to create dba by Mallory • 0
Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …
Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
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