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96 results • Page
2 of 2
Sort: Views
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Views
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Replies
1
vote
1
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158
views
ANNOVAR Download Failing
ANNOVAR
updated 2 days ago by
Ram
41k • written 2 days ago by
tony
• 0
0
votes
4
replies
147
views
Differential expression using Bowtie2
Transcriptome
Bowtie
Differential-expression
just now by
8d8fc19e
• 0
3
votes
1
reply
152
views
GEO dataset Microarray data analysis help
R
microarray
NCBI
GEO
updated 2 days ago by
Ram
41k • written 3 days ago by
Confused_human
▴ 20
0
votes
1
reply
152
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 3 days ago by
Brian Bushnell
20k • written 3 days ago by
isMM
• 0
0
votes
2
replies
152
views
How to perform quality control for sex when there are no variants after thresholding for MAF
sex
check
genetics
14 hours ago by
kl
▴ 10
0
votes
0
replies
150
views
is there a way to set colors pallets for glMDSPlot(x)?
Glimma
glMDSPlot
6 days ago by
James
• 0
0
votes
1
reply
148
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
3 days ago by
enriquesan
• 0
0
votes
0
replies
147
views
Outgroup for 1000 genomes project
haplotype
1000Genomes
phylogeny
updated 21 hours ago by
Ram
41k • written 4 months ago by
Morgan
• 0
0
votes
3
replies
147
views
Convert NCBI Downloaded files to ANNOVAR format
ANNOVAR
updated 14 hours ago by
Ram
41k • written 17 hours ago by
robert
• 0
0
votes
1
reply
144
views
Microbial gene coverage from blast result
gene
coverage
3 days ago by
aanchal.yadav
• 0
0
votes
1
reply
142
views
scRNA data analysis , how to compare pattern in multiple samples
R
scRNA
updated 21 hours ago by
Ram
41k • written 1 day ago by
Confused_human
▴ 20
0
votes
1
reply
142
views
absolute running error: Error in if (!is.na(res)) { : the condition has length > 1
ABSOLUTE
error
1 day ago by
qiuting
• 0
0
votes
2
replies
140
views
Opinion on miRNA pipeline
miRNA
pipeline
4 hours ago by
ju_ra
• 0
0
votes
0
replies
135
views
Compute matrix skipping many regions stating not found in compute matrix output
computematrix
Deeptools
6 days ago by
Mehwish
▴ 10
0
votes
0
replies
129
views
bootstraped treemix show no migration event
Treemix
Bootstrap
6 days ago by
reza
▴ 300
0
votes
0
replies
118
views
Classification ML model using different type of data
machine-learning
transcriptomics
R
python
biomarkers
3 days ago by
sil_bioinfo
▴ 40
0
votes
0
replies
118
views
Should I perform eQTL colocalization for just one of eGenes at a time?
colocalization
coloc
eCaviar
eQTL
5 days ago by
maximal_life
▴ 20
0
votes
0
replies
117
views
BioSQL Unable to remove database using server.remove_database
BioSQL
biopython
Mysql
Python
6 days ago by
Navindu
• 0
0
votes
0
replies
114
views
WGCNA for different tissues
WGCNA
Worms
RNA-Seq
2 days ago by
kdca
• 0
0
votes
0
replies
114
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 3 days ago by
Ram
41k • written 3 days ago by
boone5jones
• 0
1
vote
1
reply
112
views
recommend gene ranking methods when doing GSEA
Gene_rank
GSEA
updated 19 hours ago by
rpolicastro
12k • written 21 hours ago by
luckyday1661
• 0
0
votes
1
reply
110
views
how to draw the valcano plot for DEGs in a different way
valcano
plot
DEGs
updated 9 hours ago by
CTLong
▴ 30 • written 13 hours ago by
luckyday1661
• 0
0
votes
0
replies
108
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
3 days ago by
Saad Khan
▴ 420
0
votes
1
reply
104
views
Does orthofinder allow more than one proteome per species as input ?
comparative-genomics
orthology
updated 21 hours ago by
Ram
41k • written 23 hours ago by
Sara
• 0
0
votes
0
replies
104
views
ASEReadCounter output wrong number of coverage
ASEReadCounter
2 days ago by
junhuili
• 0
0
votes
1
reply
103
views
Funannotate iprscan Creates empty file
funannotate
interproscan
fungus
annotation
4 days ago by
Umer
▴ 50
0
votes
2
replies
102
views
Where to download excel file to include major human disease, prevalence and incidence?
Disease
Burden
updated 3 hours ago by
GenoMax
136k • written 6 hours ago by
Shicheng Guo
★ 9.3k
0
votes
0
replies
102
views
Enzyme commission number in ncbi Gene database
enzyme-commission-number
updated 2 days ago by
Ram
41k • written 3 days ago by
Maatary
• 0
0
votes
0
replies
99
views
spatial metabolomics, python
spatial-metabolomics
updated 2 days ago by
Ram
41k • written 2 days ago by
joha
▴ 10
0
votes
0
replies
99
views
megablast taxonomy assign in blobtools
blobtools
2 days ago by
bs
• 0
0
votes
0
replies
99
views
Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
3 days ago by
Adrian
• 0
0
votes
0
replies
98
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
3 days ago by
S
• 0
0
votes
0
replies
98
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
3 days ago by
Clayton
• 0
0
votes
0
replies
94
views
Comparing 16S rRNA (culture) sequences with metagenome
metagenome
shotgun
rRNA_culture
16S
updated 3 days ago by
Ram
41k • written 3 days ago by
aswin
• 0
0
votes
0
replies
89
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
3 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
89
views
cosinoRmixedeffect: an R package for mixed-effects cosinor models
interactionmodel
cosinor
mixedeffect
circadian
1 day ago by
Agnia
• 0
0
votes
0
replies
84
views
inverse normal p-value combination results giving NaN.
inverse
meta-Analysis
p-value
rnaseq
normal
1 day ago by
sehriban.buyukkilic
• 0
0
votes
0
replies
83
views
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
ATAC-seq
3 days ago by
cyril-cros
▴ 940
0
votes
0
replies
75
views
how to run GSEA with spesific background
RNA-seq
GSEA
updated 21 hours ago by
Ram
41k • written 23 hours ago by
Chava
• 0
0
votes
0
replies
64
views
use GEOparse to download series supplemental files?
gse
geoparse
python
geoquery
geo
19 hours ago by
mk
▴ 290
0
votes
0
replies
63
views
Confusing results from FindConservedMarkers in Seurat
10XGenomics
18 hours ago by
pm2012
▴ 140
0
votes
0
replies
54
views
Converting txt.gz to PLINK bim
S-LDSC
file
LDSC
format
10 hours ago by
X
• 0
0
votes
0
replies
49
views
how to label Histological regions on the H&E images in 10x visium H&E images
region
transcriptome
label
spatial
7 hours ago by
naodaigua_weng
• 0
0
votes
0
replies
32
views
How to properly mock a (Pysam) read
pysam
2 hours ago by
ManuelDB
▴ 80
0
votes
1
reply
22
views
Normalization of RNA captureSeq data (<20 genes captured)
captureSeq
edgeR
DESeq2
RNA
ERCC
updated 1 hour ago by
ATpoint
78k • written 1 hour ago by
jips
• 0
0
votes
0
replies
12
views
Error: Failed to open /ROH/.log. Try changing the --out parameter.
plink
ROH
1 hour ago by
sevda
• 0
96 results • Page
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Recent Votes
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: how to remove multiple columns from a file in R
Answer: how to remove multiple columns from a file in R
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Comment: Differential expression using Bowtie2
by
8d8fc19e
• 0
Ok, thanks for letting me know. What would you do if you wanted to compare differential expression of a gene across tissues from RNA-seq da…
Comment: SQL request from NCBI metadata and stat_analysis tables
by
marie.harmel
• 0
To put it more simply with another example, I try to display every possible order for every phyla founded in my run but I don't find the l…
Comment: SQL request from NCBI metadata and stat_analysis tables
by
marie.harmel
• 0
Thank you for your answer but unfortunately I tried it and it makes the same kind of ouptut as mine, with multtiple new (false) lines (spl…
Comment: Normalization of RNA captureSeq data (<20 genes captured)
by
ATpoint
78k
What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
Dear [Brian][1] I realized that problem is with callvariants.sh script because when I called variants using freebayes I did not find aforem…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴ 10
Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
Answer: Efficient way of calculating the number of mismatches between two sets of sequen
by
j.gleixner
• 0
Since all your sequences have the same length (say M) and you are only looking concerned with hamming distance you can encode your sequence…
Comment: Where to download excel file to include major human disease, prevalence and inci
by
GenoMax
136k
ChatGPT says Disease Prevalence Approximate Number of Cases (Worldwide) Cardiovascular Diseases High Over 17 million deaths annual…
Comment: Where to download excel file to include major human disease, prevalence and inci
by
Pierre Lindenbaum
158k
using wikidata: https://query.wikidata.org/sparql?query=%0ASELECT%20%3Fitem%20%3FitemLabel%20%3FitemDescription%20%3Fprevalence%20%3Fdoid%0…
Comment: Opinion on miRNA pipeline
by
ju_ra
• 0
Thank you very much! I see you decided to go for Bowtie as aligner. Do you see any issue in using STAR (as a splice aware reader technicall…
Answer: How to avoid missannotated GO terms?
by
Elisabeth Gasteiger
★ 2.3k
Please contact the UniProt helpdesk whenever you find such annotations, especially in these cases where the GO evidence/source tag says "Un…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
Pierre Lindenbaum
158k
again, it's a problem with the variant caller, which is ?
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴ 10
Not only opposite case but same case nucleotides are also present in vcf fle. ![enter image description here][1] [1]: /media/images/4…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴ 10
Yes [Pierre][1] there is lower case **g** in **REF** and upper case **G** in **ALT** field. My question is that why variant caller is calli…
Answer: gatk SelectVariants is giving error while extracting SNPs out of vcf file
by
Pierre Lindenbaum
158k
This is an error in your input vcf file. The REF allele MUST be différent from the ALT allele.
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