Showing : diffHic • reset
4
votes
20
replies
2.5k
views
scaling loess curves
HiTC gothic diffhic HiC
8.7 years ago Bogdan ▴ 670
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
0
votes
10
replies
1.9k
views
error running presplit_map.py
diffHic
6.6 years ago Eichan • 0
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
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
2
votes
7
replies
1.3k
views
diffHic: minimum counts per bin
diffhic edger
7.5 years ago andreucat91 • 0
1
vote
7
replies
1.7k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 4.8 years ago by ★ 28k • written 4.8 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
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
0
votes
6
replies
1.7k
views
diffHic preparepairs issue
diffhic
8.7 years ago fine418 • 0
1
vote
5
replies
1.3k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
7.8 years ago Vivek.b ▴ 100
1
vote
5
replies
1.7k
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
1
vote
4
replies
1.1k
views
diffHic:Fails to load bam file during preparePairs
diffhic
7.7 years ago manjulathimma • 0
2
votes
4
replies
1.8k
views
diffHic-package_PreparePairs-function-error:"missing chromosomes in cut site list"
diffHic PreparePairs Hi-c cutGenome
9.0 years ago • updated 8.9 years ago rulicosentino • 0
1
vote
4
replies
1.3k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 7.6 years ago by 66k • written 7.6 years ago by • 0
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
0
votes
3
replies
4.3k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 6.5 years ago by • 0 • written 8.6 years ago by • 0
0
votes
3
replies
908
views
Error in plotDI in pacakge diffHic
diffHic plotDI
7.7 years ago Andrew • 0
1
vote
3
replies
1.2k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
8.5 years ago roladali ▴ 20
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 4.9 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
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
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
1
vote
3
replies
1.1k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 130
0
votes
3
replies
1.2k
views
diffHic: alternative input?
diffhic
7.8 years ago chiara.a.nicoletti • 0
0
votes
2
replies
812
views
Can't normalize samples in diffHic
diffHic
2.9 years ago arielpaulson ▴ 20
0
votes
2
replies
1.5k
views
diffHiC read loss when loading BAM to HDF
diffhic
updated 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
0
votes
2
replies
1000
views
generate ContactMatrix from InteractionSet object
diffhic
7.7 years ago kamal.fartiyal84 ▴ 10
1
vote
2
replies
942
views
Removing trended biases between HiC libraries
diffhic
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 130
3
votes
2
replies
2.4k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
6.9 years ago e.jacobson ▴ 10
2
votes
2
replies
1.4k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
6.8 years ago sergio.espeso-gil • 0
0
votes
2
replies
743
views
Pre-processing for diffHiC
diffHiC
updated 5.6 years ago by ★ 28k • written 5.6 years ago by 66k
0
votes
2
replies
919
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
1
vote
2
replies
891
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
872
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
2.9 years ago nelsonmo • 0
0
votes
1
reply
663
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
0
votes
1
reply
889
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
882
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
1
reply
791
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 20
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
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
1
reply
854
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
922
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
1
reply
930
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 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 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
1
vote
1
reply
1.5k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 130
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
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 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 30
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 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
0
votes
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
50 results • Page 1 of 1
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Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by BioinfGuru ▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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