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96 results • Page
1 of 2
Sort: Rank
Rank
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Votes
Replies
0
votes
0
replies
15
views
recommend gene ranking methods when doing GSEA
Gene_rank
GSEA
52 minutes ago by
luckyday1661
• 0
0
votes
0
replies
18
views
Opinion on miRNA pipeline
miRNA
pipeline
1 hour ago by
ju_ra
• 0
0
votes
0
replies
15
views
SQL request from NCBI metadata and stat_analysis tables
SQL
NCBI
1 hour ago by
marie.harmel
• 0
0
votes
1
reply
38
views
Does orthofinder allow more than one proteome per species as input ?
comparative-genomics
orthology
updated 10 minutes ago by
Ram
41k • written 2 hours ago by
Sara
• 0
1
vote
4
replies
69
views
select unique samples in R
statistics
r
biostatistics
updated 57 minutes ago by
bk11
★ 1.8k • written 2 hours ago by
Bioinfonext
▴ 440
0
votes
0
replies
26
views
how to run GSEA with spesific background
RNA-seq
GSEA
updated 10 minutes ago by
Ram
41k • written 2 hours ago by
Chava
• 0
0
votes
1
reply
47
views
How to create box plot with mean and other details(color, dimension, etc. ) R
R
boxplot
updated 10 minutes ago by
Ram
41k • written 2 hours ago by
satva72
• 0
0
votes
0
replies
39
views
inverse normal p-value combination results giving NaN.
inverse
meta-Analysis
p-value
rnaseq
normal
4 hours ago by
sehriban.buyukkilic
• 0
0
votes
1
reply
65
views
Read count vs Depth
Bedtools
updated 10 minutes ago by
Ram
41k • written 5 hours ago by
Mary
• 0
0
votes
1
reply
105
views
scRNA data analysis , how to compare pattern in multiple samples
R
scRNA
updated 10 minutes ago by
Ram
41k • written 9 hours ago by
Confused_human
▴ 20
0
votes
1
reply
113
views
absolute running error: Error in if (!is.na(res)) { : the condition has length > 1
ABSOLUTE
error
6 hours ago by
qiuting
• 0
0
votes
0
replies
58
views
cosinoRmixedeffect: an R package for mixed-effects cosinor models
interactionmodel
cosinor
mixedeffect
circadian
14 hours ago by
Agnia
• 0
2
votes
3
replies
177
views
Annotation Visualization IGV
igv
alignment
gff
annotation
visualization
updated 19 hours ago by
Pierre Lindenbaum
158k • written 20 hours ago by
awhale01
• 0
0
votes
3
replies
164
views
Curated model organism gene functional annotations
Interpro
C.elegans
GO-terms
updated 1 hour ago by
manaswwm
▴ 490 • written 1 day ago by
ian.will
▴ 10
2
votes
4
replies
320
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
1 day ago by
cucindarko51
• 0
0
votes
2
replies
170
views
Very low successfully assigned alignments with feature counts
featureCounts
RNA-seq
updated 23 hours ago by
Istvan Albert
99k • written 1 day ago by
Manuel
• 0
0
votes
0
replies
83
views
ASEReadCounter output wrong number of coverage
ASEReadCounter
1 day ago by
junhuili
• 0
1
vote
1
reply
1.1k
views
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
RNAseq
updated 1 day ago by
charles.feigin
• 0 • written 6 weeks ago by
xinrantian
▴ 20
0
votes
0
replies
89
views
megablast taxonomy assign in blobtools
blobtools
1 day ago by
bs
• 0
0
votes
1
reply
154
views
Aligning sequences with multiple genetic codes!
genetic_codes
codon
MEGA11
alignment
updated 1 day ago by
5heikki
11k • written 1 day ago by
George X.
• 0
0
votes
1
reply
154
views
Cell ranger multi for demultiplexing FB files and GEX files
cellranger
updated 23 hours ago by
Ram
41k • written 1 day ago by
Shloka
• 0
0
votes
1
reply
160
views
Software for Spatial Transcriptomic data [NanoString; Visium]?
NanoString
Visium
Spatial-Transcriptomics
10X
1 day ago by
LauferVA
3.8k
1
vote
1
reply
148
views
ANNOVAR Download Failing
ANNOVAR
updated 1 day ago by
Ram
41k • written 1 day ago by
tony
• 0
0
votes
1
reply
162
views
Sorted bam files are empty after sorting them from bam
bam
dna
updated 1 day ago by
Ram
41k • written 1 day ago by
mgranada3
▴ 30
0
votes
2
replies
212
views
Downsampling ATAC-seq BAM files
ATAC-seq
1 day ago by
Elise
• 0
0
votes
0
replies
98
views
spatial metabolomics, python
spatial-metabolomics
updated 1 day ago by
Ram
41k • written 1 day ago by
joha
▴ 10
1
vote
4
replies
223
views
Feasibility of Enrichment Analysis from RTqPCR results
GO
RT-qPCR
Enrichment-Analysis
updated 1 day ago by
GenoMax
136k • written 2 days ago by
Javier
• 0
0
votes
0
replies
114
views
WGCNA for different tissues
WGCNA
Worms
RNA-Seq
2 days ago by
kdca
• 0
0
votes
1
reply
176
views
Contrasts in R
contrasts
r
updated 1 day ago by
jv
★ 1.3k • written 2 days ago by
SGMS
▴ 130
0
votes
1
reply
519
views
How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes
MLST
phylogenetic
nanopre
updated 2 days ago by
Joe
21k • written 2 days ago by
Ralph
• 0
0
votes
1
reply
157
views
How to remove 3rd codon positions in a multiple sequence allignment?
i
updated 1 day ago by
Ram
41k • written 2 days ago by
francesco.degiglio
• 0
0
votes
0
replies
116
views
Classification ML model using different type of data
machine-learning
transcriptomics
R
python
biomarkers
2 days ago by
sil_bioinfo
▴ 40
0
votes
0
replies
103
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
2 days ago by
Saad Khan
▴ 420
0
votes
0
replies
97
views
Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
2 days ago by
Adrian
• 0
3
votes
1
reply
150
views
GEO dataset Microarray data analysis help
R
microarray
NCBI
GEO
updated 1 day ago by
Ram
41k • written 2 days ago by
Confused_human
▴ 20
0
votes
3
replies
204
views
Microarray batch correction method suggestions
microarray
batch-correction
updated 1 day ago by
Ram
41k • written 2 days ago by
Sumeet
• 0
0
votes
0
replies
95
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
2 days ago by
Clayton
• 0
0
votes
0
replies
101
views
Enzyme commission number in ncbi Gene database
enzyme-commission-number
updated 1 day ago by
Ram
41k • written 2 days ago by
Maatary
• 0
0
votes
1
reply
148
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 2 days ago by
Brian Bushnell
20k • written 2 days ago by
isMM
• 0
2
votes
4
replies
267
views
error when installing gistic2 using conda
conda
gistic2
updated 1 day ago by
Ram
41k • written 2 days ago by
luckyday1661
• 0
0
votes
0
replies
112
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 2 days ago by
Ram
41k • written 2 days ago by
boone5jones
• 0
0
votes
0
replies
95
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
2 days ago by
S
• 0
0
votes
2
replies
202
views
what should I do if I get a compromised sample of scRNA-seq data?
scRNA-seq
data
snRNA-seq
updated 2 days ago by
ATpoint
78k • written 2 days ago by
wangjb702
• 0
0
votes
0
replies
94
views
Comparing 16S rRNA (culture) sequences with metagenome
metagenome
shotgun
rRNA_culture
16S
updated 2 days ago by
Ram
41k • written 2 days ago by
aswin
• 0
0
votes
4
replies
270
views
Filling gaps in BAM file
bamtools
samtools
gene
bam
updated 1 day ago by
seidel
11k • written 2 days ago by
hemr3
• 0
0
votes
1
reply
146
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
2 days ago by
enriquesan
• 0
1
vote
5
replies
273
views
vcftools
vcftools
updated 2 days ago by
Barista
▴ 10 • written 2 days ago by
sevda
• 0
0
votes
0
replies
82
views
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
ATAC-seq
2 days ago by
cyril-cros
▴ 940
0
votes
1
reply
142
views
Microbial gene coverage from blast result
gene
coverage
2 days ago by
aanchal.yadav
• 0
0
votes
0
replies
87
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
3 days ago by
Assa Yeroslaviz
★ 1.8k
96 results • Page
1 of 2
Recent Votes
A: Gene set enrichment analysis with logFC and PValue
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Answer: convert dataframe R
Answer: convert dataframe R
Answer: Get gene names from rs SNP ids
How to query 1000 genomes project VCF files for specific regions without downloading whole chromosomes first?
Answer: How to add exon annotations to genome annotation
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Recent Awards •
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Scholar
to
fracarb8
★ 1.3k
Popular Question
to
bioinfo
▴ 140
Popular Question
to
bk11
★ 1.8k
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Agamemnon
▴ 80
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cmdcolin
★ 3.4k
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satva72
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Recent Replies
Answer: How to avoid missannotated GO terms?
by
Istvan Albert
99k
The problem most likely is with the blast alignment. BLAST is a local aligner, getting a hit to another sequence does not mean that the…
Comment: Read count vs Depth
by
Ram
41k
Do not use spreadsheet software to view plain text files. Use a plain text utility such as BBEdit/TextWrangler/NotePad++/gedit or simple co…
Comment: How to create box plot with mean and other details(color, dimension, etc. ) R
by
Ram
41k
Please stop asking basic R/programming questions and use Google to learn the underlying concepts. Your best bet to create customized plots …
Comment: vcftools
by
Ram
41k
What output files were you expecting? Was nothing printed on the screen at all?
Comment: Consensus peaksets in DiffBind - conceptual questinos
by
Rory Stark
★ 2.0k
The question of defaults for the software is often a tricky one. I do think the mutliple-replicate method is a good idea in many cases, w…
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
by
Pierre Lindenbaum
158k
bcftools works with remote indexed VCF bcftools view "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_cov…
Comment: Consensus peaksets in DiffBind - conceptual questinos
by
Sam
▴ 300
My question was not how to do it - but conceptually, should not this be the default way to do an analysis, unless there is a good reason *n…
Comment: select unique samples in R
by
bk11
★ 1.8k
Instead of `setdiff(list1$Sample_ID, list2$Sample_ID)` do this- `setdiff(list1, list2)`
Answer: Consensus peaksets in DiffBind - conceptual questinos
by
Rory Stark
★ 2.0k
What you describe - deriving a consensus set comprising the union of peaks called in at least two replicates of any sample group - is exact…
Comment: convert dataframe R
by
satva72
• 0
Thanks
Comment: select unique samples in R
by
Matthias Zepper
4.2k
Then you use the resulting IDs to subset your original data frame(s).
Comment: convert dataframe R
by
fracarb8
★ 1.3k
You need to pass a column, so `id.vars = "rows"` should work.
Comment: convert dataframe R
by
satva72
• 0
Thanks. there is this error: "Error in melt.data.table(data, id.vars = rownames(data)) : One or more values in 'id.vars' is invalid." T…
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
by
Jeremy Leipzig
22k
We have the 3202 samples from the 1kg DRAGEN called high coverge gVCFs on TileDB. If you sign up there we can get you some credits and assi…
Answer: convert dataframe R
by
fracarb8
★ 1.3k
More a programming question than bioinfo, but using `data.table` you can library(data.table) df <-as.data.frame(matrix(runif(100,…
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