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122,200 results • Page
618 of 2444
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0
votes
3
replies
1.2k
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Differential expression design considerations
RNA-Seq
Limma
DE
Differential_Expression
4.4 years ago by
bioinf.questions
• 0
2
votes
1
reply
1.3k
views
Multiple BAM files (ccs) input with Lima (PacBio)
Long-read-sequencing
PacBio
updated 19 months ago by
Ram
45k • written 4.4 years ago by
aa9gj
▴ 10
0
votes
0
replies
1.0k
views
RNA-seq raw counts normalization for survival analysis
survival
tcga
RNA-Seq
r
4.4 years ago by
fifty_fifty
▴ 90
0
votes
1
reply
1.0k
views
Statistic Method Question: How to display correlation from pheatmap with other data
RNA-seq
correlation
Bioconductor
pheatmap
updated 4.4 years ago by
dioscorea.bulbifera
▴ 10 • written 4.4 years ago by
Qamarul
• 0
0
votes
2
replies
1.4k
views
alternatives to replication for GWAS
replication
discovery
GWAS
4.4 years ago by
putty
▴ 40
2
votes
0
replies
1.0k
views
Tool:
metaGEM: create your own genome scale metabolic models directly from metagenomes
metagenomics
metagenome-assembled-genome
genome-scale-metabolic-model
metabolism
updated 4.4 years ago by
Ram
45k • written 4.4 years ago by
metagenomez
▴ 20
0
votes
2
replies
1.2k
views
Queries regarding Network analysis of Differentially expressed genes.
Network-analysis
Stringdb
updated 2.7 years ago by
Ram
45k • written 4.4 years ago by
Saransh
• 0
0
votes
2
replies
1.1k
views
transfer parameter to reader group in bwa mem command
bwa
4.4 years ago by
Chenfei Zheng
▴ 60
2
votes
2
replies
1.2k
views
R programming: basics to challenging
R
updated 4.4 years ago by
ATpoint
90k • written 4.4 years ago by
pixie@bioinfo
★ 1.5k
1
vote
0
replies
1.9k
views
Job:
Bioinformatician with software engineering skills at DTU Biosustain
SQL
GitHub
updated 2.7 years ago by
Ram
45k • written 4.4 years ago by
info
▴ 90
0
votes
2
replies
1.5k
views
How can I do hypothesis test for continuous dependent variable and two categorical independent variabables which are related?
variable
categorical
Metagenome
statics
updated 4.4 years ago by
Lemire
▴ 940 • written 4.4 years ago by
BioDH
▴ 10
2
votes
2
replies
2.0k
views
Format GISTIC2 all_data_by_genes.txt and cBioPortal
copy
number
output
format
gistic2
cbioportal
updated 4 months ago by
Ram
45k • written 4.4 years ago by
mike.rightmire
▴ 20
0
votes
1
reply
1.4k
views
Highlight unique transcripts in Gviz
gviz
updated 4.4 years ago by
C.
• 0 • written 5.5 years ago by
peris_baba
▴ 20
0
votes
6
replies
5.5k
views
The exon numbers of each transcript,
RNA
exon
4.4 years ago by
haasroni
• 0
0
votes
3
replies
2.7k
views
shows the expression of genes in specific cell types in Heatmap
dittoseq
RNA-seq
Seurat
updated 4.4 years ago by
Wocher33
▴ 10 • written 4.4 years ago by
Maria17
▴ 40
0
votes
1
reply
1.9k
views
Error: samtools sort: failed to read header from "-" ARTIC Pipeline for SAR-COV-2
artic
NGS
nanopore
updated 2.7 years ago by
Ram
45k • written 4.4 years ago by
Pratibha kadam
• 0
0
votes
15
replies
4.9k
views
SAMFormatException: Did not inflate expected amount error
WES
updated 4.0 years ago by
greekkey
▴ 30 • written 4.4 years ago by
smrutimayipanda
▴ 20
0
votes
0
replies
1.1k
views
How to perform Z-score normalization for Cox-regression analysis, based on signature enrichment within TCGA data?
cox-regression
ssGSEA
TCGA
Z-score
normalization
4.4 years ago by
joker33
▴ 150
0
votes
0
replies
946
views
hclust2.py heatmap in MetaPhlAn3 --ftop features
MetaPhlAn3
Data-Analysis
WholeShotgunMetagenome
Microbiome
Metagenomics
4.4 years ago by
serene.s
• 0
0
votes
0
replies
861
views
AGeNT LocatIt
AGeNT
LocatIt
UMI
duplicates
GATK
4.4 years ago by
jhy
▴ 10
2
votes
1
reply
1.4k
views
Subset vcf on info field
bcftools
vcftools
vcf
clinvar
updated 4.4 years ago by
Pierre Lindenbaum
166k • written 4.4 years ago by
gevikoj888
• 0
0
votes
2
replies
11k
views
Applying hard filters for variants
variants
variant-calling
GATK
snps
updated 3.3 years ago by
Ram
45k • written 10.0 years ago by
bioinforesearchquestions
▴ 370
1
vote
2
replies
3.4k
views
RSeQC python runtime errors for tin.py
RNA-Seq
sequencing
software error
updated 4.4 years ago by
chasem
▴ 50 • written 7.5 years ago by
freuv
▴ 20
0
votes
0
replies
1.1k
views
Significance Test for Fst Values
fst
DNaSP
MEGA
significance
population
4.4 years ago by
kacollier
▴ 30
0
votes
0
replies
867
views
CheckVCF.py error question
Michigan-server
SNP
Quality-Control
updated 2.7 years ago by
Ram
45k • written 4.4 years ago by
ErickW
• 0
1
vote
2
replies
1.4k
views
Identify conserved regions in SARS-COV2 virus based on Multiple sequence alignment for primer design
alignment
MSA
conserved
primer
design
sequence
Multiple
region
4.4 years ago by
Mohamed Elsherbieny
• 0
0
votes
0
replies
888
views
How to properly interpret the ALT and QUAL fields in bcf file from bcftools mpileup
bcftools
DNA-seq
mpileup
4.4 years ago by
gt
▴ 30
0
votes
0
replies
2.0k
views
Job:
Senior Scientist of Computational Genomics in Johnson & Johnson
analysis
genetics
genomics
4.4 years ago by
Shicheng Guo
★ 9.6k
5
votes
5
replies
2.8k
views
how to remove a substring for multiple file names?
string
bash
2.8 years ago by
v.berriosfarias
▴ 140
0
votes
0
replies
658
views
error related to predixcan
PrediXcan
TWAS
MetaXcan
SNP
4.4 years ago by
rheab1230
▴ 150
5
votes
6
replies
3.3k
views
How to get 'chr' prefix hg38 reference genome
HG38
human
reference
chr
updated 4.4 years ago by
GenoMax
154k • written 4.4 years ago by
alan
▴ 10
1
vote
4
replies
1.4k
views
scRNA: special help
scRNA
updated 2.7 years ago by
Ram
45k • written 4.4 years ago by
ConfusedSheep
▴ 10
3
votes
3
replies
2.1k
views
Very high Beta coefficients in --glm output in plink2
glm
Beta
plink2
updated 3.1 years ago by
LauferVA
4.8k • written 4.4 years ago by
putty
▴ 40
1
vote
1
reply
961
views
Cell cycle gene list for Rat
RNA
Seurat
rat
sequencing
10x
updated 4.4 years ago by
ATpoint
90k • written 4.4 years ago by
Lauren
• 0
5
votes
4
replies
3.5k
views
fgsea returns empty dataframe
GSEA
NMF
R
fgsea
gene-expression
4.4 years ago by
charlielonergan
▴ 20
0
votes
3
replies
1.4k
views
Several contigs hit the same species with viralComplete : which contigs should I use to map the reads with bowtie2?
contigs
bowtie2
viralComplete
metagenomics
updated 4.4 years ago by
andres.firrincieli
3.9k • written 4.4 years ago by
bioAddict
• 0
0
votes
0
replies
832
views
What are the minimal contig length and kmer coverage below which I should drop some contigs in viral metagenomics study after assembly with Spades?
Kmer
Length
Contigs
coverage
Metagenomics
4.4 years ago by
bioAddict
• 0
0
votes
0
replies
739
views
No significant gene sets in gene set enrichment analysis using the R package iDEA
gse
iDEA
mouse
4.4 years ago by
Stevens
▴ 30
1
vote
0
replies
699
views
Expression Profiling by array in Geo Datasets (Normalization)
Profiling
Expression
updated 3.0 years ago by
Ram
45k • written 4.4 years ago by
David
▴ 30
0
votes
0
replies
1.6k
views
Job:
Postdocs @ New York City: Long Reads Epigenomics, Metagenomics and Transcriptomics
epigenomics
splicing
assembly
sequencing
microbiome
4.4 years ago by
fanggang
▴ 120
1
vote
0
replies
2.2k
views
pre-imputation allele frequency check against HRC reference panel
QC
imputation
pre-imputation
TOPMed
updated 4.4 years ago by
GenoMax
154k • written 4.4 years ago by
psb7
▴ 20
6
votes
6
replies
3.0k
views
Genome-wide heterozygosity
heterozygosity
genome
4.1 years ago by
gubrins
▴ 350
1
vote
3
replies
1.4k
views
BEDtools: intersect bed on delly v0.7.8 VCF output
SV
bedtools
intersectbed
delly
VCF
4.4 years ago by
Helena
• 0
3
votes
4
replies
2.0k
views
PCA for combined set
plink
bcftools
vcf
PCA
4.4 years ago by
raalsuwaidi
▴ 110
2
votes
3
replies
1.6k
views
Description (of at least top levels) of Gene Ontology hierarchy ?
GO
4.4 years ago by
Alexander
▴ 220
5
votes
3
replies
14k
views
deseq2 replicates error
R
RNA-Seq
updated 4.4 years ago by
Nai
▴ 50 • written 5.7 years ago by
Balatheskulter
• 0
0
votes
1
reply
956
views
Viral Amplicon Haplotype Calling
gatk
freebayes
illumina
paired-end
amplicon
4.4 years ago by
geneticatt
▴ 140
1
vote
4
replies
1.7k
views
Filter bam file AND header
filter
header
BAM
4.4 years ago by
quentin54520
▴ 120
1
vote
3
replies
1.9k
views
Picard Markduplicates and samtools markdup Issues with samtools view and htseq
Markduplicates
Picard
RNASeq
samtools
updated 4.4 years ago by
Pierre Lindenbaum
166k • written 4.4 years ago by
aka
▴ 10
17
votes
11
replies
14k
views
8 follow
How to input data for DESeq2 from individual HTSeq count?
RNA-Seq
HTSeq
rna-seq
deseq
deseq2
updated 4.4 years ago by
swbarnes2
15k • written 7.1 years ago by
sudu87
▴ 40
122,200 results • Page
618 of 2444
Recent Votes
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
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Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
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Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
Pierre Lindenbaum
166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome?
by
alexandrakortsi
• 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
xinguok794
▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics
by
Kent
▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around
by
Luca Arbore
▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets
by
GenoMax
154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets
by
DrSmad
▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types
by
shpak.max
▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets
by
GenoMax
154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat
by
yura.grabovska
▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
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