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questions
0
votes
0
replies
438
views
Which are the best Cell - Cell communication packages for single cell RNASeq timeseries data?
R
scrna
seurat
24 months ago by
AB
▴ 360
7
votes
3
replies
2.9k
views
Extending and clipping bed files
ChIP-Seq
bedtools
updated 2.5 years ago by
chunshi
• 0 • written 8.0 years ago by
AB
▴ 360
0
votes
4
replies
3.1k
views
Database of mouse ligand receptors
ligand-receptor
database
mm9
updated 3.0 years ago by
zhang
• 0 • written 7.0 years ago by
AB
▴ 360
2
votes
1
reply
3.0k
views
results from SNPSift Concordance
SNPSift
concordance
snp
updated 3.1 years ago by
sara.wennersten
• 0 • written 7.4 years ago by
AB
▴ 360
1
vote
3
replies
2.8k
views
Error :[[<- defined for objects of type "S4" only for subclasses of environment - Shiny App error
shiny
Seurat
single cell RNASeq
3.7 years ago by
AB
▴ 360
3
votes
2
replies
5.4k
views
Error when using Bedtools fisher on sorted bed files
ChIP-Seq
bedtools
fisher test
updated 3.8 years ago by
chrisclarkson100
▴ 160 • written 8.6 years ago by
AB
▴ 360
3
votes
2
replies
1.3k
views
Aligning multiple runs using STARSolo
single cell RNASeq
scRNA
STARSolo
STAR
Alignment
updated 3.9 years ago by
ATpoint
84k • written 3.9 years ago by
AB
▴ 360
0
votes
3
replies
1.9k
views
sratoolkit prefetch command returns no result
sratoolkit
updated 3.9 years ago by
ATpoint
84k • written 3.9 years ago by
AB
▴ 360
2
votes
1
reply
4.2k
views
Downloading single cell RNASeq data using SRA
single-cell-RNASeq
sratoolkit
updated 15 months ago by
Ram
44k • written 4.0 years ago by
AB
▴ 360
0
votes
1
reply
1.0k
views
Identifying appearance or disappearance of cell populations between WT and Mut single cell RNA-Seq data
single cell RNA-Seq
Seurat
updated 4.3 years ago by
igor
13k • written 4.3 years ago by
AB
▴ 360
3
votes
3
replies
8.5k
views
Saving 3D plot from rgl as a pdf
rgl
3dplot
5.4 years ago by
AB
▴ 360
3
votes
8
replies
12k
views
converting vcf to text file
vcf
eqtl
Matrix EQTL
updated 5.6 years ago by
Biostar
20 • written 6.9 years ago by
AB
▴ 360
0
votes
1
reply
1.5k
views
Count empty rows in Rhandsontable
rhandsontable
shiny
5.9 years ago by
AB
▴ 360
3
votes
6
replies
4.6k
views
Error while running pfamscan.pl : Unable to translate nucleotide sequences to protein sequences
RNA-Seq
PfamScan
lincRNA
updated 6.0 years ago by
Ram
44k • written 8.6 years ago by
AB
▴ 360
0
votes
1
reply
1.4k
views
Error displaying GTEX like boxplot in UCSC Genome Browser - "Error creating boxplot from sample data"
ucsc
genomebrowser
boxplot
GTEx Barcharts
6.0 years ago by
AB
▴ 360
8
votes
1
reply
4.8k
views
Converting narrowpeak files to make it compatible with UCSC trackhub
ucsc
genomebrowser
narrowpeakfile
ucscutilites
6.1 years ago by
AB
▴ 360
1
vote
2
replies
4.4k
views
Classify cells using seurat
scRNA
seurat
monocle
updated 6.3 years ago by
dppb05
▴ 110 • written 6.6 years ago by
AB
▴ 360
6
votes
3
replies
5.7k
views
Log transformation of RPKM data for PCA analysis
RNA-Seq
rpkm
PCA
log-transformation
updated 2.1 years ago by
Ram
44k • written 8.9 years ago by
AB
▴ 360
2
votes
2
replies
4.9k
views
Vcf-compare two multi-sample vcf files
vcf-compare
vcftools
updated 6.7 years ago by
maduh17
▴ 10 • written 7.4 years ago by
AB
▴ 360
6
votes
6
replies
3.0k
views
UCSC Fasta files by chromosome for rn6
ucsc
fasta
rn6
updated 6.9 years ago by
genecats.ucsc
▴ 580 • written 6.9 years ago by
AB
▴ 360
3
votes
3
replies
3.1k
views
running multiple RSeQC jobs
RNA-Seq
RSeQC
tin.py
updated 7.1 years ago by
Biostar
20 • written 7.3 years ago by
AB
▴ 360
2
votes
3
replies
5.9k
views
How to increase point size or color palette of a PCA plot using the scater package for scRNA analysis
scater
plotPCA
7.2 years ago by
AB
▴ 360
0
votes
0
replies
1.2k
views
Going from Snps to exons to protein domains
snps
proteindomains
variant Effect Predictor
7.4 years ago by
AB
▴ 360
0
votes
2
replies
36k
views
"Error in contrib.url(repos, type) : trying to use CRAN without setting a mirror" Error when installing package
R
shiny-server
7.4 years ago by
AB
▴ 360
2
votes
5
replies
5.2k
views
Picard MergeSam error : Cannot use index file with textual SAM file
picard
mergesam
7.5 years ago by
AB
▴ 360
4
votes
3
replies
2.0k
views
bam-readcount : Reference_base is not the base with highest count
bam-readcount
updated 7.5 years ago by
iraun
6.2k • written 7.5 years ago by
AB
▴ 360
0
votes
0
replies
1.9k
views
Very high negative scores from bigWigAverageOverBed
ChIP-Seq
bigWigAverageOverBed
updated 7.9 years ago by
Biostar
20 • written 8.0 years ago by
AB
▴ 360
4
votes
2
replies
3.1k
views
Finding distribution of indels from vcf file
vcf
samtools
barplots
updated 8.0 years ago by
Brice Sarver
★ 3.8k • written 8.0 years ago by
AB
▴ 360
0
votes
0
replies
1.9k
views
What is a good cutoff of mappability score from bigWigAverageOverBed ?
ChIP-Seq
bigWigAverageOverBed
8.0 years ago by
AB
▴ 360
2
votes
3
replies
3.3k
views
what do negative values from bigWigAverageOverBed output mean?
ChIP-Seq
bigWigAverageOverBed
deepTools
updated 8.0 years ago by
Devon Ryan
104k • written 8.0 years ago by
AB
▴ 360
1
vote
1
reply
2.5k
views
Calculating FPKM of reads that overlap regions of interest
ChIP-Seq
fpkm
bedtools
8.1 years ago by
AB
▴ 360
9
votes
2
replies
4.9k
views
MACS2 Peak Calling : Different number of peaks for each replicate
ChIP-Seq
biological-replicates
MACS2
updated 2.2 years ago by
Ram
44k • written 8.7 years ago by
AB
▴ 360
0
votes
1
reply
1.8k
views
Finding out if non-coding transcripts from CPAT are tissue specific?
RNA-Seq
CPAT
lncRNA
updated 2.2 years ago by
Ram
44k • written 8.6 years ago by
AB
▴ 360
3
votes
6
replies
3.5k
views
Differential binding analysis of motif-containing peaks
ChIP-Seq
FIMO
DiffBind
updated 2.2 years ago by
Ram
44k • written 8.6 years ago by
AB
▴ 360
1
vote
3
replies
1.9k
views
Determine Condition using LogFC values
RNA-Seq
fold-changes
updated 2.1 years ago by
Ram
44k • written 8.8 years ago by
AB
▴ 360
0
votes
1
reply
3.3k
views
Removing batch effects from RPKM data
limma
removeBatchEffect
batch-effect
rpkm
updated 5 months ago by
Ram
44k • written 8.9 years ago by
AB
▴ 360
13
votes
6
replies
10k
views
PCA plot of RPKM data from RNA-Seq dataset
RNA-Seq
bioconductor
pca
rpkm
updated 8.9 years ago by
informatics bot
▴ 760 • written 8.9 years ago by
AB
▴ 360
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