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492 results • Page
4 of 10
Sort: Votes
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Views
Votes
Replies
0
votes
2
replies
249
views
Problem with downloading genome in SnpEff
SnpEff
17 days ago by
Javier
• 0
0
votes
1
reply
248
views
Bowtie2 alignment rate
galaxy
Bowtie
alignment-rate
updated 25 days ago by
gv
• 0 • written 29 days ago by
pavithraashokkumar818
• 0
0
votes
2
replies
317
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
14 days ago by
O.rka
▴ 710
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 10 days ago by
Ram
43k • written 6.1 years ago by
Jun
• 0
0
votes
0
replies
102
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 1 day ago by
Ram
43k • written 1 day ago by
SineWave
• 0
0
votes
0
replies
115
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 3 days ago by
Ram
43k • written 3 days ago by
newuser2024
• 0
0
votes
2
replies
415
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
8 days ago by
Ashok
• 0
0
votes
0
replies
110
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 5 days ago by
Ram
43k • written 5 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
203
views
Lncipedia GTF file error
Proteomics
updated 8 days ago by
Ram
43k • written 8 days ago by
atharvakarkare14
▴ 10
0
votes
0
replies
181
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
8 days ago by
DanielEB_fisk
▴ 20
0
votes
0
replies
299
views
Superfreq result interpretation for amplification events from RNA-Seq
rna-seq
Superfreq
cnv
updated 25 days ago by
Ram
43k • written 9 months ago by
aksh
• 0
0
votes
0
replies
168
views
Dante Labs VCF analysis, CHROM column absence UPD: solved!
vcf
coordinate
dante
assembly
chromosome
28 days ago by
k.alincha
• 0
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 9 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
0
votes
0
replies
152
views
CIBERSORT deconvolution by using long read sequencing data
long-read-sequencing
CIBERSORT
updated 22 days ago by
Ram
43k • written 22 days ago by
IVORY
• 0
0
votes
0
replies
102
views
WGCNA: analysis of complex trait associations with regression
WGCNA
25 days ago by
w.cookson
• 0
0
votes
1
reply
200
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
24 days ago by
Gordon
• 0
0
votes
0
replies
161
views
what exactly is a k-mer table (remora)?
remora
basecall
11 days ago by
anne
• 0
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 7 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
0
votes
1
reply
656
views
How to find the co ordinates of long reads (simulated by Badreads) with respect to the reference genome
long-reads
reference-genome
assembly
updated 22 days ago by
Ram
43k • written 2.7 years ago by
Ashi
▴ 20
0
votes
1
reply
516
views
Geneious vs Perl script of IN SILICO PCR
PCR
Geneious
updated 25 days ago by
Ram
43k • written 23 months ago by
Bio_Crap
• 0
0
votes
1
reply
272
views
cibersort. problem
cibersort
gema122
updated 19 days ago by
Ram
43k • written 23 days ago by
gem1
• 0
0
votes
2
replies
264
views
RNAseq 1 control 2 different treatment
RNA-seq
11 days ago by
matteo.levorato
• 0
0
votes
0
replies
117
views
Peptide Toxicity
protein
toxinpred3.0
toxicity
peptide
26 days ago by
Saurabh
• 0
0
votes
7
replies
405
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 22 days ago by
Papyrus
★ 2.9k • written 23 days ago by
doramora
▴ 10
0
votes
2
replies
267
views
WGCNA
PCA
WGCNA
EIGENGENE
15 days ago by
rajasekargutha
▴ 60
0
votes
0
replies
117
views
Blast2GO Fisher test
Fisher-test
Go-annotation
Blast2GO
updated 19 days ago by
Ram
43k • written 19 days ago by
BlackM
• 0
0
votes
0
replies
120
views
Public datasets for genome-wide level mRNA-protein correlation calculation?
correlation
protein
mRNA
16 days ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect
kbet
updated 9 days ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
0
votes
1
reply
219
views
Finding chimeric reads for CRISPR edited mouse cells from RNA-Seq data
RNA-seq
crispr
updated 26 days ago by
Haci
▴ 680 • written 29 days ago by
Ethan
• 0
0
votes
1
reply
265
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 8 days ago by
GenoMax
141k • written 8 days ago by
bioyas
▴ 10
0
votes
0
replies
89
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
1 day ago by
turcoa1
• 0
0
votes
1
reply
197
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 10 days ago by
DKA
▴ 40 • written 10 days ago by
james.melhorn
• 0
0
votes
0
replies
188
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 15 days ago by
GenoMax
141k • written 15 days ago by
zec018
• 0
0
votes
0
replies
91
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 4 days ago by
Ram
43k • written 4 days ago by
SHREYA
• 0
0
votes
0
replies
136
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
7 days ago by
Mamatha Y S
• 0
0
votes
1
reply
165
views
P-values for pairwise FST
FST
P-value
pairwise
updated 18 days ago by
dthorbur
★ 1.9k • written 18 days ago by
Emy
▴ 50
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome
PCA
batch-effect
SNP
updated 10 days ago by
Ram
43k • written 4.7 years ago by
Ace
▴ 90
0
votes
8
replies
330
views
Error in cnetplot enrichplot package
R
updated 5 days ago by
Ram
43k • written 5 days ago by
Farhad
• 0
0
votes
0
replies
1.1k
views
Extra adjustment variables during batch effect correction
rna-seq
ComBat
batch-effect
updated 10 days ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
0
votes
0
replies
144
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
12 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
88
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
5 days ago by
manaswwm
▴ 490
0
votes
1
reply
819
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 9 days ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
0
replies
111
views
R/Python function to retrieve interacted proteins from HPA database
HPA
24 days ago by
Shicheng Guo
★ 9.4k
0
votes
2
replies
264
views
bam merging for archaic samples
samtools
bam
updated 6 days ago by
Ram
43k • written 7 days ago by
Matteo Ungaro
▴ 100
0
votes
3
replies
323
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 14 days ago by
ATpoint
82k • written 16 days ago by
gdfsnkfns
• 0
0
votes
1
reply
167
views
How do I run fastq-dump on multiple prefetched files at once?
sratoolkit
fastq-dump
updated 20 days ago by
Pierre Lindenbaum
161k • written 20 days ago by
biotrekker
▴ 100
0
votes
0
replies
250
views
What does it means, when 2-direction perturbed pathways are identified in the gage enrichment analysis?
r
pathway
go-enrichment
gage
25 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
5
replies
436
views
Error running local blastn in R using system2
blastn
NCBI
R
29 days ago by
Harrison
• 0
0
votes
0
replies
206
views
Copy number variation plot
Copy-number-variation
genomics
updated 8 days ago by
Ram
43k • written 8 days ago by
Emmi
• 0
0
votes
0
replies
111
views
Variant Calling for one gene - Stage of filtering
gatk
picard
variant-calling
updated 25 days ago by
Ram
43k • written 25 days ago by
andrebolerbarros
• 0
492 results • Page
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correcting for a batch in DESeq2
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
NGS forensics: how to know if data is fabricated
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Comment: NGS forensics: how to know if data is fabricated
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> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
Comment: ScRNAseq-How to correctly choose cell type marker genes
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Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated
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> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated
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My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
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[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
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Use the standalone version of Nextflow and specify the process-specific conda environments paths.
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can you show us an exonic position in your VCF file that is all `./.`?
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Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
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I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
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just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
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Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
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features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
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Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
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