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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
1
reply
161
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 1 day ago by
CTLong
▴ 20 • written 4 days ago by
e.iich
• 0
0
votes
3
replies
229
views
merged rs number information
merged
dbsnp
3 days ago by
sskimvd
• 0
1
vote
1
reply
163
views
Beginner differential methylation analysis
Methylation
updated 3 days ago by
Basti
★ 1.9k • written 4 days ago by
a.basitkhan1990
▴ 30
2
votes
1
reply
236
views
EnhancedVolcano underrepresenting DEGs
R
updated 2 days ago by
Kevin Blighe
86k • written 4 days ago by
jabbari.parnian
▴ 30
0
votes
0
replies
111
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
4 days ago by
jiazheng_lin
• 0
0
votes
0
replies
124
views
Negative F statistics for sex check in plink
plink
check
sex
4 days ago by
kl
▴ 10
0
votes
1
reply
193
views
Chipseq peak calling and peak frequency region
chipseeker
macs2
updated 3 days ago by
Arup Ghosh
3.2k • written 5 days ago by
Mehwish
▴ 10
0
votes
1
reply
247
views
issue in RNA -seq analysis
NGS
RNA-Seq
updated 5 days ago by
GenoMax
136k • written 5 days ago by
subhiksha
• 0
0
votes
3
replies
341
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 5 days ago by
ATpoint
78k • written 6 days ago by
manuelmourato25
• 0
0
votes
0
replies
226
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
6 days ago by
Wenke
• 0
0
votes
3
replies
301
views
Annovar - Annotated file cells show string
annovar
6 days ago by
Roshan
• 0
0
votes
1
reply
242
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW
MinION
Nanopore
updated 6 days ago by
GenoMax
136k • written 6 days ago by
Soumajit
▴ 40
0
votes
1
reply
214
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
updated 1 day ago by
Ram
41k • written 6 days ago by
bioinfo
▴ 60
0
votes
0
replies
157
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA
Worms
RNA-Seq
6 days ago by
kdca
• 0
0
votes
3
replies
273
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
6 days ago by
Sara
▴ 230
0
votes
0
replies
879
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics
telomeres
reads
6 days ago by
Mark
• 0
0
votes
0
replies
155
views
not best k value found
de
assemblly
assembly
novo
kmergenie
6 days ago by
shaileshdesai76
• 0
0
votes
0
replies
166
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR
ribo-seq
multi-mapped
rna-seq
TE
7 days ago by
Carmen
• 0
0
votes
0
replies
170
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq
deseq2
7 days ago by
pl23
• 0
0
votes
2
replies
285
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
2 days ago by
je71xusa
• 0
0
votes
2
replies
275
views
Tool to get genes in the neighbourhood of a particular gene
locus
Gene
updated 7 days ago by
Raony Guimarães
★ 1.3k • written 7 days ago by
ThePlaintiff
▴ 80
2
votes
9
replies
655
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
1 day ago by
ian.will
▴ 10
5
votes
2
replies
245
views
RNA Contamination Tool for Developing Cell Samples
contamination
scRNA
quality
RNA
SoupX
6 days ago by
Rafael Soler
★ 1.2k
1
vote
2
replies
199
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole
genome
assembly
sequencing
updated 7 days ago by
WouterDeCoster
47k • written 7 days ago by
manaswiniparija3
▴ 10
1
vote
0
replies
140
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics
proteomics
multiomics
8 days ago by
WUSCHEL
▴ 720
0
votes
3
replies
296
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 2 days ago by
jv
★ 1.2k • written 8 days ago by
TC_Chang
▴ 10
0
votes
0
replies
112
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway
mapping
database
8 days ago by
Ngrin
• 0
0
votes
0
replies
126
views
GenAlEx Haploid Data Detecting Recombination
GenAlEx
Popgen
Haploid
Recombination
8 days ago by
turcoa1
• 0
0
votes
0
replies
130
views
TF Footprinting using HINT ATAC module from RGT
hintatac
footprinting
rgttoolbox
atacseq
8 days ago by
alphaflylizard
• 0
0
votes
2
replies
261
views
Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA
translation
Variant
proteomics
FASTA
VCF
7 days ago by
chscho
• 0
0
votes
0
replies
118
views
Trouble making a ggmsa alignment plot
R
ggmsa
8 days ago by
andre.arrudalima
▴ 30
0
votes
0
replies
112
views
cNMF vs LIGER
NMF
correction
batch
8 days ago by
e.r.zakiev
▴ 170
1
vote
4
replies
301
views
Analyze with Geo2R
R
NCBI
6 days ago by
anasjamshed
▴ 120
0
votes
0
replies
869
views
For people doing high molecular weight DNA sequencing library prep, do you see a steep drop off in the fragment sizes before and after the library pr…
library-prep
sequencing
ont
nanopore
ngs
8 days ago by
Mark
• 0
0
votes
0
replies
129
views
Creating heatmap for ChIP-seq using deeptools
heatmap
chipseq
chip
deeptools
visualization
8 days ago by
biology_inform
▴ 50
0
votes
1
reply
138
views
error in plink
polygenicriskscore
prscalculation
prs
plink
error
updated 8 days ago by
biofalconch
★ 1.1k • written 8 days ago by
Emilija
• 0
0
votes
2
replies
209
views
how to use pilon
genome
pipelines
assembly
pilon
contig
updated 3 days ago by
Arup Ghosh
3.2k • written 8 days ago by
vasudhapai
• 0
3
votes
2
replies
241
views
t-test by row
R
t-test
updated 8 days ago by
dthorbur
▴ 880 • written 9 days ago by
sooni
▴ 10
0
votes
0
replies
110
views
jellyfish histo is empty
jellyfish
kmer
fastq
9 days ago by
m.t.lorenc
• 0
0
votes
0
replies
123
views
Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject
giraffe
surject
vg
9 days ago by
cassiwatt
• 0
1
vote
2
replies
209
views
How to identify the nearest gene associated with a specific SNPs?
RSID
GWAS
updated 9 days ago by
Jeremy
▴ 840 • written 9 days ago by
camillab.
▴ 150
0
votes
1
reply
168
views
WGCNA convenience function
WGCNA
updated 8 days ago by
andres.firrincieli
3.5k • written 9 days ago by
fluentin44
• 0
0
votes
0
replies
120
views
Low mapping after Cufflinks assembly
assembly
gffread
cuffmerge
Cufflinks
RSEM
9 days ago by
sofiablancoglez
• 0
0
votes
0
replies
115
views
KEGG module and abundance of its KEGG Orthologs for functioning
function
kegg
abundance
9 days ago by
Jonathan Yoou
▴ 60
1
vote
4
replies
278
views
Deseq2 5 level condition - building contrast
rna-seq
deseq2
updated 9 days ago by
ATpoint
78k • written 9 days ago by
annaA
▴ 10
0
votes
0
replies
114
views
RNASeq vs TermSeq
RNAseq
statistics
TermSeq
9 days ago by
npb27
• 0
0
votes
0
replies
107
views
Best Preprocessing Approach for Tissue Microarray Data: Separate or Post-Merger Normalization?
normalization
array
9 days ago by
rk.khayami94
▴ 10
0
votes
0
replies
112
views
Interpretation of mean-variance trend in voom
EdgeR
Voom
updated 9 days ago by
Ram
41k • written 9 days ago by
Ivana
• 0
0
votes
0
replies
168
views
How to perform analysis with given copy number variation datasets between disease and control cohorts
CNV
analysis
9 days ago by
Tsin-Lau
• 0
0
votes
0
replies
114
views
Pathview Enzyme Code to Gene Symbol Conversion
Pathview
KEGG
10 days ago by
B.N.
• 0
1,000 results • Page
2 of 20
Recent Votes
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
Seurat integration of two datasets - GSE126783
about batch correction in scRNA-seq
How to compare two Seurat object (sample) in order to find top markers?
How do I resolve an integration error in Seurat?
The difference between merge and integration with Seurat objects
Analyzing single cell RNA seq with multiple samples and conditions
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Peerzada
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mohammedtoufiq91
▴ 230
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★ 2.2k
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wiscoyogi
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Recent Replies
Comment: How can I map coordinates between two strains of yeast?
by
Jimmy
▴ 10
Yes (S. cerevisiae)
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
GenoMax
136k
> less than 100 for some samples Hmm. That is surprising but then in light of that fact ~20% recovery of cells does not sound bad.
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
newbee
▴ 40
Thanks for raising these valid points. I do not have the answer right now. Lately, I heard from the PI that they started with a small numbe…
Comment: How to get multiple protein domain database domain name from id's
by
GenoMax
136k
A list of InterPro domains is available: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
Answer: DIAMOND tutorial
by
GenoMax
136k
`DIAMOND` has a wiki page: https://github.com/bbuchfink/diamond/wiki Links for DIAMOND papers are here: https://github.com/bbuchfink/diamo…
Comment: How to do simple pathway analysis?
by
AK
★ 2.2k
Hi [he1k](https://www.biostars.org/u/139817/), Please use the following script which downloads and parses the keg data on the fly: [keg_hi…
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's what I would assume, because we are not taking into account cross sample differences here. Thanks
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's a good point. So its probably safest to not batch correct for within sample comparisons I guess?
Answer: Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cel
by
MohammadAlkadi
▴ 70
What is the purpose of doing so? I tried to do that by using the bam file generated by CellRanger. One **important detail** if you are work…
Comment: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Thank you - appreciate the translation.
Answer: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Em geral, uma taxa de descoberta falsa de 5% (p ajustado<0,05 ) deve ser usada para qualquer teste estatístico em que múltiplas hipóteses i…
Answer: WGCNA tutorial docs needed: Horvath Lab site down
by
ATpoint
78k
See link here from the developer: https://bioinformatics.stackexchange.com/a/21886/16676
Comment: WGCNA tutorial docs needed: Horvath Lab site down
by
Katie
• 0
I would also appreciate the PDFs if anyone has them please
Answer: Loftee no splice site annotations
by
AMARU
• 0
Hey, did you solve it? I am having a very similar issue. Thanks
Answer: Bulk and Single Cell RNA-seq online course
by
swbarnes2
13k
I'd start by getting tutorials for R libraries like DESeq, EdgeR, Seurat, etc, and learn by doing.
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