Showing : diffhic • reset
2
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diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
3.8 years ago nelsonmo • 0
0
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2
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1.1k
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Can't normalize samples in diffHic
diffHic
3.8 years ago arielpaulson ▴ 20
1
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7
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2.0k
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problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 30
0
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1
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1.2k
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How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
0
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1
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896
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diffHiC error in mergePairs.
diffHiC rdhf5
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
0
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1
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1.4k
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conda install of diffHic
diffHic conda
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
1
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7
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2.2k
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Error while running normOffsets in diffhic
diffhic csaw
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
1
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2
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1.2k
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rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
0
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3
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1.5k
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diffHic presplit_map.py --sig option for HiC libraries prepared with restriction enzyme cocktail from Arima genomics
diffhic Arima Genomics presplit_map.py
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
2
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3
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1.3k
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diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
5.8 years ago shopnil99 • 0
0
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2
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1.3k
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diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 10
0
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9
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2.0k
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from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 10
0
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1
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1.2k
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Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
6.4 years ago mictadlo ▴ 10
0
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2
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959
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Pre-processing for diffHiC
diffHiC
updated 6.5 years ago by ★ 28k • written 6.5 years ago by 68k
1
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1
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1.8k
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extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
0
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3
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4.9k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 7.4 years ago by • 0 • written 9.5 years ago by • 0
2
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1
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1.5k
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Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 20
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3
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1.6k
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csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 7.5 years ago by 25k • written 7.5 years ago by • 0
0
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8
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2.1k
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How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 20
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10
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2.5k
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error running presplit_map.py
diffHic
7.5 years ago Eichan • 0
2
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2
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1.7k
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Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
7.7 years ago sergio.espeso-gil • 0
3
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2
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2.9k
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Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
7.8 years ago e.jacobson ▴ 10
0
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1
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896
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How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
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6
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1.7k
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min enrichment in peak calling with diffHiC?
diffhic peak
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 20
2
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1
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1.5k
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diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 20
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1
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1.2k
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diffHic count data
diffhic
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 10
2
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7
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1.6k
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diffHic: minimum counts per bin
diffhic edger
8.4 years ago andreucat91 • 0
5
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12
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3.7k
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How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
8.4 years ago Sameet Mehta ▴ 30
1
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2
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1.1k
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Removing trended biases between HiC libraries
diffhic
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ▴ 130
1
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3
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1.3k
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Interpreting strand orientation plots in diffHic
diffhic
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ▴ 130
1
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4
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1.6k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 8.5 years ago by 68k • written 8.5 years ago by • 0
0
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3
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1.1k
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Error in plotDI in pacakge diffHic
diffHic plotDI
8.6 years ago Andrew • 0
0
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1
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1.4k
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 8.6 years ago by ★ 28k • written 8.6 years ago by • 0
1
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4
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1.3k
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diffHic:Fails to load bam file during preparePairs
diffhic
8.7 years ago • updated 8.6 years ago manjulathimma • 0
0
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2
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1.2k
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generate ContactMatrix from InteractionSet object
diffhic
8.6 years ago kamal.fartiyal84 ▴ 10
1
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3
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1.8k
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diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 8.7 years ago by • 0 • written 8.7 years ago by • 0
1
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5
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1.7k
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diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
8.7 years ago Vivek.b ▴ 100
0
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3
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1.4k
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diffHic: alternative input?
diffhic
8.8 years ago • updated 8.7 years ago chiara.a.nicoletti • 0
0
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1
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1.2k
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diffHic preparePairs function
diffHic
updated 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
0
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1
reply
1.1k
views
diffHiC: Error when call preparePairs
diffhic
updated 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
0
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1
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1.1k
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diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
0
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1
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976
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diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 20
1
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3
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1.3k
views
diffHiC preparePairs error
diffhic preparepairs
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 20
0
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1
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1.1k
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diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 8.9 years ago by ★ 28k • written 8.9 years ago by • 0
1
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1
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1.8k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 130
1
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5
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2.1k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 9.2 years ago by ★ 28k • written 9.2 years ago by • 0
0
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1
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1.2k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 9.4 years ago by ★ 28k • written 9.4 years ago by • 0
0
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1
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1.2k
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 9.4 years ago by ★ 28k • written 9.4 years ago by • 0
1
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3
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1.4k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
9.5 years ago roladali ▴ 20
0
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6
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2.0k
views
diffHic preparepairs issue
diffhic
9.6 years ago fine418 • 0
50 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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