Showing : diffhic • reset
2
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1.1k
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diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
3.6 years ago nelsonmo • 0
0
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2
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1.1k
views
Can't normalize samples in diffHic
diffHic
3.7 years ago • updated 3.6 years ago arielpaulson ▴ 20
1
vote
7
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2.0k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 30
0
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1
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1.1k
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
0
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1
reply
868
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diffHiC error in mergePairs.
diffHiC rdhf5
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
0
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1
reply
1.4k
views
conda install of diffHic
diffHic conda
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
1
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7
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2.2k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
1
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2
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1.1k
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
0
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3
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1.4k
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 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
2
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3
replies
1.3k
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
5.6 years ago shopnil99 • 0
0
votes
2
replies
1.2k
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 10
0
votes
9
replies
1.9k
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 10
0
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1
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1.1k
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
6.3 years ago • updated 6.2 years ago mictadlo ▴ 10
0
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2
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939
views
Pre-processing for diffHiC
diffHiC
updated 6.4 years ago by ★ 28k • written 6.4 years ago by 68k
1
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1
reply
1.7k
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
0
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3
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4.7k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 7.3 years ago by • 0 • written 9.4 years ago by • 0
2
votes
1
reply
1.5k
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 20
0
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3
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1.6k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 7.4 years ago by 25k • written 7.4 years ago by • 0
0
votes
8
replies
2.0k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 20
0
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10
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2.4k
views
error running presplit_map.py
diffHic
7.4 years ago Eichan • 0
2
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2
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1.7k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
7.6 years ago sergio.espeso-gil • 0
3
votes
2
replies
2.8k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
7.7 years ago • updated 7.6 years ago e.jacobson ▴ 10
0
votes
1
reply
881
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
6
replies
1.6k
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 20
2
votes
1
reply
1.5k
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 20
0
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1
reply
1.1k
views
diffHic count data
diffhic
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 10
2
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7
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1.6k
views
diffHic: minimum counts per bin
diffhic edger
8.2 years ago andreucat91 • 0
5
votes
12
replies
3.6k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
8.2 years ago Sameet Mehta ▴ 30
1
vote
2
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1.1k
views
Removing trended biases between HiC libraries
diffhic
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 130
1
vote
3
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1.3k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 130
1
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4
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1.5k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
0
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3
replies
1.1k
views
Error in plotDI in pacakge diffHic
diffHic plotDI
8.5 years ago Andrew • 0
0
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1
reply
1.3k
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
1
vote
4
replies
1.3k
views
diffHic:Fails to load bam file during preparePairs
diffhic
8.5 years ago manjulathimma • 0
0
votes
2
replies
1.2k
views
generate ContactMatrix from InteractionSet object
diffhic
8.5 years ago kamal.fartiyal84 ▴ 10
1
vote
3
replies
1.7k
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 8.5 years ago by • 0 • written 8.5 years ago by • 0
1
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5
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1.6k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
8.6 years ago Vivek.b ▴ 100
0
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3
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1.3k
views
diffHic: alternative input?
diffhic
8.6 years ago chiara.a.nicoletti • 0
0
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1
reply
1.2k
views
diffHic preparePairs function
diffHic
updated 8.6 years ago by ★ 28k • written 8.6 years ago by • 0
0
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1
reply
1.1k
views
diffHiC: Error when call preparePairs
diffhic
updated 8.7 years ago by ★ 28k • written 8.7 years ago by • 0
0
votes
1
reply
1.1k
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 8.7 years ago by ★ 28k • written 8.7 years ago by • 0
0
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1
reply
949
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 20
1
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3
replies
1.3k
views
diffHiC preparePairs error
diffhic preparepairs
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 20
0
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1
reply
1.1k
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
1
vote
1
reply
1.7k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 130
1
vote
5
replies
2.0k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 9.1 years ago by ★ 28k • written 9.1 years ago by • 0
0
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1
reply
1.2k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 9.3 years ago by ★ 28k • written 9.3 years ago by • 0
0
votes
1
reply
1.2k
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 9.3 years ago by ★ 28k • written 9.3 years ago by • 0
1
vote
3
replies
1.4k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
9.3 years ago roladali ▴ 20
0
votes
6
replies
1.9k
views
diffHic preparepairs issue
diffhic
9.5 years ago • updated 9.4 years ago fine418 • 0
50 results • Page 1 of 1
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Answer: Differential expression of proteins using somascan data by James W. MacDonald 68k
Providing a bunch of code but not the output is not very helpful. Ideally you would just provide ``` nrow(design) ncol(protein_data_lo…
Comment: Surprising behavior for DEXseq dispersion estimate plot? by Elijah • 0
Hi Snow, Thanks for your comment! I didn't do any normalization of the counts prior to the DEXseq pipeline - I've only been using the inte…
Comment: Using tximport for kallisto aligned TOIL data by Nicholas • 0
Sorry, I misspoke. The data was from the TOIL project and was aligned using kallisto. It was accessed from the UCSC XENA browser. I updated…
Comment: Using tximport for kallisto aligned recount2 data by ATpoint ★ 4.7k
recount 2 does not use kallisto, does it? And recount does offer genelevel counts, so what's the point?
Comment: Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package by Yao Lipu • 0
Thank you for your help! Your explanation was very clear and really helped me solve my issue. I truly appreciate your time and effort!
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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