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44 results • Page
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0
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200
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want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs.
DEGs
updated just now by
jv
▴ 780 • written 2 days ago by
rupali
• 0
0
votes
0
replies
2
views
snp Caenorhabditis elegans
download
Caenorhabditis
snp
elegans
4 minutes ago by
haiminabox
• 0
0
votes
0
replies
3
views
Dealing with missing (NA) values in my 450K methylation array dataset
minfi
PCA
expression
Methylation
R
11 minutes ago by
Edward E-B
• 0
0
votes
0
replies
13
views
Mapping IDs to systematic names (GOSim, setevidencelevel() )
GOSim
1 hour ago by
eliska.ochodkova
• 0
0
votes
3
replies
46
views
What type of database does gnomAD use?
gnomAD
genomics
database
updated 1 hour ago by
Matthias Zepper
2.9k • written 2 hours ago by
Mariana Ribeiro
• 0
0
votes
1
reply
29
views
Novogene somatic results with GATK mutect2
Mutect2
Novogene
GATK
somatic
VCF
updated 48 minutes ago by
GenoMax
125k • written 2 hours ago by
chrisgr
▴ 20
0
votes
4
replies
52
views
fastqc: Per base sequence content
illumina
metagenomic
fastqc
updated 8 minutes ago by
jv
▴ 780 • written 3 hours ago by
khoojj
• 0
0
votes
0
replies
35
views
A question about Bioinformatik analysis and experimental design / comparing 2 experiments
effect
good
Batch
experiments
DEseq2
comparing
conduct
3 hours ago by
Frederik
• 0
4
votes
3
replies
64
views
Is it possible to do bedtools multicov across the entire genome?
bedtools
depth
hg38
3 hours ago by
amy__
▴ 50
0
votes
1
reply
83
views
Index with unmasked or masked in HISAT2
masked
HISAT2
toplevel
unmasked
updated 3 hours ago by
GenoMax
125k • written 8 hours ago by
ibq.enriquepola
• 0
1
vote
1
reply
94
views
How to enable multiple cores/threads for Bowtie2 or BWA using Macbook M2 chip?
mac
bowtie2
bwa
m2
updated 3 hours ago by
GenoMax
125k • written 7 hours ago by
weixiaokuan
▴ 130
1
vote
2
replies
232
views
Obtaining every"Protein ID" from a genome in OMA
OMA
orthologs
updated 4 hours ago by
Adrian Altenhoff
★ 1.0k • written 2 days ago by
christyh
• 0
0
votes
1
reply
89
views
Error, (in LoadSpliceMap) string to parse is too long
oma
LoadSpliceMap
omastandalone
orthology
updated 4 hours ago by
Adrian Altenhoff
★ 1.0k • written 11 hours ago by
ziqing
• 0
2
votes
1
reply
184
views
How to use CAFE from Orthofinder Results
expansion
orthofinder
cafe
gene
updated 5 hours ago by
dariober
14k • written 1 day ago by
ahmadjoyyia
▴ 10
0
votes
0
replies
68
views
Input data for LIMMA: unnormalised or vsn or other?
lima
normalisation
vns
5 hours ago by
Sebastian Hesse
▴ 320
0
votes
2
replies
160
views
how to get an average ROC curve after 10-fold cross validation in r
r
cross-validation
curve
roc
updated 3 hours ago by
GenoMax
125k • written 18 hours ago by
Lisa
• 0
0
votes
0
replies
57
views
question of exonerate output
protein
gff
exonerate
annotation
7 hours ago by
TN
• 0
2
votes
0
replies
75
views
CircRNA extraction from bulk RNA seq datasets using CIRCexplorer2 with STAR alignment
alignment
CIRCexplorer2
STAR
7 hours ago by
choijamtsm
▴ 60
1
vote
1
reply
186
views
Tripal installation question
BioDb
Drush
Tripal
Drupal
9 hours ago by
alslonik
▴ 260
2
votes
2
replies
235
views
Can Singularity be installed on a single-node server or does it have to be HPC?
Singularity
updated 12 hours ago by
tothepoint
▴ 720 • written 1 day ago by
SalmaElShafie
• 0
0
votes
0
replies
83
views
Mis-paired primers
amplicon
primers
Mis-paired
14 hours ago by
Sara
▴ 10
0
votes
0
replies
73
views
show amplicon like exon in UCSC/IGV
amplicon
15 hours ago by
Sara
▴ 10
0
votes
2
replies
142
views
scATAC-seq workflow
Signac
scATAC-seq
18 hours ago by
bioinformatics.girl
• 0
0
votes
0
replies
105
views
Set Y limits for ggplot with sec.axis
rstudio
ggplot
22 hours ago by
JirMan
• 0
0
votes
0
replies
110
views
MetaboAnalyst: Interpreting Enrichment Analysis Results
enrichment
metabolomics
22 hours ago by
eva_u
▴ 10
0
votes
5
replies
350
views
ceres score in crispr screen
ceres
crispr
ngs
3 hours ago by
edus_bioinfo
▴ 20
0
votes
0
replies
170
views
Issues Using DMRcate and rmSNPandCH
DMRcate
R
just now by
Indira
• 0
0
votes
3
replies
264
views
How to find the most frequent alternative-splicing event from DEXSEQ data?
DESEQ
RNA-SEQ
DEXSEQ
updated 5 hours ago by
i.sudbery
16k • written 1 day ago by
STARDUST
• 0
2
votes
6
replies
358
views
RNA Editing data from RNA-seq
Editing
RNA
13 minutes ago by
Genetics
• 0
0
votes
6
replies
408
views
PLINK2 selecting variants based on INFO score
plink2
5 hours ago by
m.c.roozen
• 0
0
votes
3
replies
357
views
DESeq2 results function runs very slow on Windows 10
r
deseq2
updated 23 hours ago by
i.sudbery
16k • written 2 days ago by
Taha
• 0
3
votes
5
replies
445
views
High downstream gene expression
downstream
High
Gene
expression
updated 23 hours ago by
i.sudbery
16k • written 3 days ago by
yoser4
▴ 10
0
votes
5
replies
265
views
Clustering and dynamic tree cutting
dynamicTreeCut
Clustering
data
RNAseq
cutreeDynamic
updated 2 hours ago by
andres.firrincieli
3.1k • written 3 days ago by
harish
• 0
0
votes
5
replies
342
views
RNASeq differential expression masked by pathways disregulation
normalization
Rnaseq
batch
1 hour ago by
Gama313
▴ 110
0
votes
0
replies
93
views
why count_matrix.csv generated by "prepDE.py3" showed unidentified IDs
Stringtie
RNA-seq
21 hours ago by
Pegasus
▴ 40
0
votes
5
replies
300
views
Protein protein interactions
protein
partners
interacting
interaction
3 hours ago by
Peerzada
• 0
38
votes
12
replies
20k
views
12 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq
DESeq2
geneontology
GSEA
updated 5 hours ago by
Lada
▴ 10 • written 5.3 years ago by
Sreeraj Thamban
▴ 280
0
votes
1
reply
158
views
How to choose --mind value for plink SNPs filtering
SNPs
mind
plink
filter
updated 18 hours ago by
Fabio Marroni
★ 2.9k • written 6 days ago by
anithanagaraj93
• 0
3
votes
4
replies
430
views
Question on how to filter DESeq2 results correctly and use of the results function
RNA-seq
DEseq2
3 hours ago by
Frederik
• 0
1
vote
1
reply
276
views
open source webserver for multi-omics data store and descriptional visualization
webserver
multi-omics
open-source
updated 4 minutes ago by
Matthias Zepper
2.9k • written 4 weeks ago by
Zhilong Jia
★ 2.1k
1
vote
2
replies
350
views
PHG database building for very large genomes
phg
4 hours ago by
twrl8
• 0
4
votes
26
replies
15k
views
10 follow
ADMIXTURE and R, color meaning on barplot in studing population ancestry, K value
R
gene
updated 9 hours ago by
dr.fakharunnisa
• 0 • written 7.4 years ago by
dirranrak
▴ 20
1
vote
7
replies
1.6k
views
ballgown and pData
RNA-Seq
ballgown
updated 9 hours ago by
Pegasus
▴ 40 • written 3.6 years ago by
Morris_Chair
▴ 330
2
votes
5
replies
1.9k
views
Error in reading ballgown object
RNA-Seq
R
ballgown
updated 8 hours ago by
Pegasus
▴ 40 • written 5.1 years ago by
amy16
▴ 40
44 results • Page
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Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Comment: RNA Editing data from RNA-seq
Comment: RNA Editing data from RNA-seq
CircRNA extraction from bulk RNA seq datasets using CIRCexplorer2 with STAR alignment
Does Gene length corrected TMM [GeTMM] violate any assumptions of TMM normalization?
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Comment: fastqc: Per base sequence content
by
jv
▴ 780
I think this is to be expected based a report I was able to find online <https://uu.diva-portal.org/smash/get/diva2:1608120/FULLTEXT01.pd…
Comment: fastqc: Per base sequence content
by
GenoMax
125k
Unless the kit directions tell you to remove remove the initial 10-15 bp you may as well leave them alone. Data should align would be my in…
Comment: RNA Editing data from RNA-seq
by
Genetics
• 0
Thank you so much for your kind reply and for helping a bioinformatics beginner like me. Can I use **bowtie2** tools for allignment and th…
Comment: fastqc: Per base sequence content
by
khoojj
• 0
Yes, I have proceed with analysis but I wonder if it is necessary to remove the first 10 or so bp from the reads. I have checked that NEBN…
Comment: Novogene somatic results with GATK mutect2
by
GenoMax
125k
Did you look in the header of the provided VCF to see if any information has been encoded there (e.g. command line/options used).
Comment: RNASeq differential expression masked by pathways disregulation
by
Gama313
▴ 110
That's exactly what I've done. However the dispersion is really high (primary samples) and the total number of samples seems really low to…
Comment: fastqc: Per base sequence content
by
GenoMax
125k
If the library was made using tagmentation then you will see that pattern. Flag warnings on FastQC do not immediately indicate that the da…
Answer: What type of database does gnomAD use?
by
Matthias Zepper
2.9k
I suppose there are multiple? Queries via Hail are very likely run against a [Matrix Table][1], but the web application likely uses a diffe…
Comment: What type of database does gnomAD use?
by
Pierre Lindenbaum
152k
> I have my own data, so I would like to try to create my own type of exome aggregation database, and the idea was to try to replicate gnom…
Answer: What type of database does gnomAD use?
by
Pierre Lindenbaum
152k
Google Cloud SDK https://github.com/broadinstitute/gnomad-browser/tree/main/deploy , but previous versions used mongodb https://github.com/…
Comment: Clustering and dynamic tree cutting
by
andres.firrincieli
3.1k
I don't think the `cutreeDynamic` function will work very well with a distance matrix calculated from pearson correlation values: `as.matri…
Comment: Clustering and dynamic tree cutting
by
harish
• 0
These are differentially expressed genes, which are around 15K genes from a total of 30 K genes. Then I follow the clustering protocol as g…
Comment: ceres score in crispr screen
by
edus_bioinfo
▴ 20
I solved the issue with using bowtie. But now I am experiencing this issue; > Error in makeGRangesFromDataFrame(., seqinfo = genomeinfo, k…
Comment: Protein protein interactions
by
Peerzada
• 0
Sir, How much time does this server take to give output for 1 pair of proteins as I have submitted several hours ago and it still shows ru…
Comment: Question on how to filter DESeq2 results correctly and use of the results functi
by
Frederik
• 0
Thanks alot :)
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