Showing : diffhic • reset
0
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3
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4.3k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 6.4 years ago by • 0 • written 8.5 years ago by • 0
5
votes
12
replies
2.9k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
7.4 years ago Sameet Mehta ▴ 30
4
votes
20
replies
2.4k
views
scaling loess curves
HiTC gothic diffhic HiC
8.6 years ago Bogdan ▴ 670
3
votes
2
replies
2.3k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
6.8 years ago e.jacobson ▴ 10
0
votes
10
replies
1.9k
views
error running presplit_map.py
diffHic
6.5 years ago Eichan • 0
2
votes
4
replies
1.7k
views
diffHic-package_PreparePairs-function-error:"missing chromosomes in cut site list"
diffHic PreparePairs Hi-c cutGenome
8.9 years ago • updated 8.8 years ago rulicosentino • 0
1
vote
5
replies
1.7k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
0
votes
6
replies
1.7k
views
diffHic preparepairs issue
diffhic
8.6 years ago fine418 • 0
1
vote
7
replies
1.6k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
1
vote
7
replies
1.6k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 30
0
votes
8
replies
1.6k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 20
1
vote
1
reply
1.5k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 120
0
votes
2
replies
1.5k
views
diffHiC read loss when loading BAM to HDF
diffhic
updated 8.7 years ago by ★ 28k • written 8.7 years ago by • 0
0
votes
9
replies
1.5k
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 10
2
votes
2
replies
1.4k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
6.7 years ago sergio.espeso-gil • 0
1
vote
3
replies
1.4k
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 7.7 years ago by • 0 • written 7.7 years ago by • 0
1
vote
1
reply
1.3k
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
1
vote
5
replies
1.3k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
7.7 years ago Vivek.b ▴ 100
1
vote
4
replies
1.3k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 7.5 years ago by 65k • written 7.5 years ago by • 0
0
votes
6
replies
1.3k
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 20
0
votes
3
replies
1.3k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
2
votes
7
replies
1.2k
views
diffHic: minimum counts per bin
diffhic edger
7.4 years ago andreucat91 • 0
2
votes
1
reply
1.2k
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 20
2
votes
1
reply
1.2k
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 20
1
vote
3
replies
1.2k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
8.5 years ago roladali ▴ 20
2
votes
1
reply
1.2k
views
How to read in bam file that is output from presplit_map.py using the GenomicAlignment package
diffhic
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 30
0
votes
3
replies
1.1k
views
diffHic: alternative input?
diffhic
7.8 years ago • updated 7.7 years ago chiara.a.nicoletti • 0
1
vote
4
replies
1.1k
views
diffHic:Fails to load bam file during preparePairs
diffhic
7.7 years ago • updated 7.6 years ago manjulathimma • 0
0
votes
1
reply
1.1k
views
conda install of diffHic
diffHic conda
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
1
vote
3
replies
1.1k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 120
0
votes
1
reply
1.1k
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
0
votes
1
reply
1.1k
views
DiffHic-package. Identify the name of bins with over or underrepresentation of reads mapped -marginCounts- . Extracting data from DIList objects
MarginCounts squareCounts DIList DiffHic
updated 8.7 years ago by ★ 28k • written 8.7 years ago by • 0
0
votes
1
reply
1.1k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
1
vote
3
replies
1.0k
views
diffHiC preparePairs error
diffhic preparepairs
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 20
0
votes
1
reply
1.0k
views
diffHic preparePairs function
diffHic
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
3
replies
1.0k
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 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
2
votes
3
replies
1.0k
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
4.8 years ago shopnil99 • 0
0
votes
1
reply
1000
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
0
votes
2
replies
981
views
generate ContactMatrix from InteractionSet object
diffhic
7.6 years ago kamal.fartiyal84 ▴ 10
0
votes
1
reply
973
views
diffHic count data
diffhic
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 10
1
vote
2
replies
924
views
Removing trended biases between HiC libraries
diffhic
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 120
0
votes
1
reply
914
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
1
reply
902
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
5.4 years ago mictadlo ▴ 10
0
votes
3
replies
894
views
Error in plotDI in pacakge diffHic
diffHic plotDI
7.6 years ago Andrew • 0
0
votes
2
replies
894
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
0
votes
1
reply
875
views
diffHiC: Error when call preparePairs
diffhic
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
1
reply
869
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
1
vote
2
replies
864
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
2
votes
2
replies
844
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
2.8 years ago nelsonmo • 0
0
votes
1
reply
826
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
50 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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