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121,832 results • Page
610 of 2437
Sort: Rank
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Votes
Replies
0
votes
0
replies
961
views
RNA-seq raw counts normalization for survival analysis
survival
tcga
RNA-Seq
r
4.1 years ago by
fifty_fifty
▴ 90
0
votes
1
reply
903
views
Statistic Method Question: How to display correlation from pheatmap with other data
RNA-seq
correlation
Bioconductor
pheatmap
updated 4.1 years ago by
dioscorea.bulbifera
▴ 10 • written 4.1 years ago by
Qamarul
• 0
0
votes
2
replies
1.2k
views
alternatives to replication for GWAS
replication
discovery
GWAS
4.1 years ago by
putty
▴ 40
2
votes
0
replies
909
views
Tool:
metaGEM: create your own genome scale metabolic models directly from metagenomes
metagenomics
metagenome-assembled-genome
genome-scale-metabolic-model
metabolism
updated 4.1 years ago by
Ram
45k • written 4.1 years ago by
metagenomez
▴ 20
0
votes
2
replies
1.0k
views
Queries regarding Network analysis of Differentially expressed genes.
Network-analysis
Stringdb
updated 2.5 years ago by
Ram
45k • written 4.1 years ago by
Saransh
• 0
0
votes
2
replies
986
views
transfer parameter to reader group in bwa mem command
bwa
4.1 years ago by
Chenfei Zheng
▴ 60
2
votes
2
replies
1.1k
views
R programming: basics to challenging
R
updated 4.1 years ago by
ATpoint
89k • written 4.1 years ago by
pixie@bioinfo
★ 1.5k
1
vote
0
replies
1.8k
views
Job:
Bioinformatician with software engineering skills at DTU Biosustain
SQL
GitHub
updated 2.5 years ago by
Ram
45k • written 4.1 years ago by
info
▴ 80
0
votes
2
replies
1.4k
views
How can I do hypothesis test for continuous dependent variable and two categorical independent variabables which are related?
variable
categorical
Metagenome
statics
updated 4.1 years ago by
Lemire
▴ 940 • written 4.1 years ago by
BioDH
▴ 10
2
votes
2
replies
1.8k
views
Format GISTIC2 all_data_by_genes.txt and cBioPortal
copy
number
output
format
gistic2
cbioportal
updated 6 weeks ago by
Ram
45k • written 4.1 years ago by
mike.rightmire
▴ 20
0
votes
1
reply
1.2k
views
Highlight unique transcripts in Gviz
gviz
updated 4.1 years ago by
C.
• 0 • written 5.2 years ago by
peris_baba
▴ 20
0
votes
6
replies
4.7k
views
The exon numbers of each transcript,
RNA
exon
4.1 years ago by
haasroni
• 0
0
votes
3
replies
2.5k
views
shows the expression of genes in specific cell types in Heatmap
dittoseq
RNA-seq
Seurat
updated 4.1 years ago by
Wocher33
▴ 10 • written 4.1 years ago by
Maria17
▴ 40
0
votes
1
reply
1.8k
views
Error: samtools sort: failed to read header from "-" ARTIC Pipeline for SAR-COV-2
artic
NGS
nanopore
updated 2.5 years ago by
Ram
45k • written 4.1 years ago by
Pratibha kadam
• 0
0
votes
15
replies
4.6k
views
SAMFormatException: Did not inflate expected amount error
WES
updated 3.8 years ago by
greekkey
▴ 30 • written 4.2 years ago by
smrutimayipanda
▴ 20
0
votes
0
replies
1.0k
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
4.1 years ago by
joker33
▴ 150
0
votes
0
replies
872
views
hclust2.py heatmap in MetaPhlAn3 --ftop features
MetaPhlAn3
Data-Analysis
WholeShotgunMetagenome
Microbiome
Metagenomics
4.1 years ago by
serene.s
• 0
0
votes
0
replies
788
views
AGeNT LocatIt
AGeNT
LocatIt
UMI
duplicates
GATK
4.1 years ago by
jhy
▴ 10
2
votes
1
reply
1.3k
views
Subset vcf on info field
bcftools
vcftools
vcf
clinvar
updated 4.1 years ago by
Pierre Lindenbaum
166k • written 4.1 years ago by
gevikoj888
• 0
0
votes
2
replies
11k
views
Applying hard filters for variants
variants
variant-calling
GATK
snps
updated 3.1 years ago by
Ram
45k • written 9.8 years ago by
bioinforesearchquestions
▴ 370
1
vote
2
replies
3.3k
views
RSeQC python runtime errors for tin.py
RNA-Seq
sequencing
software error
updated 4.1 years ago by
chasem
▴ 50 • written 7.2 years ago by
freuv
▴ 20
0
votes
0
replies
1.1k
views
Significance Test for Fst Values
fst
DNaSP
MEGA
significance
population
4.1 years ago by
kacollier
▴ 30
0
votes
0
replies
781
views
CheckVCF.py error question
Michigan-server
SNP
Quality-Control
updated 2.5 years ago by
Ram
45k • written 4.1 years ago by
ErickW
• 0
1
vote
2
replies
1.2k
views
Identify conserved regions in SARS-COV2 virus based on Multiple sequence alignment for primer design
alignment
MSA
conserved
primer
design
sequence
Multiple
region
4.1 years ago by
Mohamed Elsherbieny
• 0
0
votes
0
replies
794
views
How to properly interpret the ALT and QUAL fields in bcf file from bcftools mpileup
bcftools
DNA-seq
mpileup
4.1 years ago by
gt
▴ 30
0
votes
0
replies
1.9k
views
Job:
Senior Scientist of Computational Genomics in Johnson & Johnson
analysis
genetics
genomics
4.1 years ago by
Shicheng Guo
★ 9.6k
5
votes
5
replies
2.6k
views
how to remove a substring for multiple file names?
string
bash
2.6 years ago by
v.berriosfarias
▴ 140
0
votes
0
replies
603
views
error related to predixcan
PrediXcan
TWAS
MetaXcan
SNP
4.1 years ago by
rheab1230
▴ 150
5
votes
6
replies
3.0k
views
How to get 'chr' prefix hg38 reference genome
HG38
human
reference
chr
updated 4.1 years ago by
GenoMax
153k • written 4.1 years ago by
alan
▴ 10
1
vote
4
replies
1.3k
views
scRNA: special help
scRNA
updated 2.5 years ago by
Ram
45k • written 4.1 years ago by
ConfusedSheep
▴ 10
3
votes
3
replies
1.9k
views
Very high Beta coefficients in --glm output in plink2
glm
Beta
plink2
updated 2.8 years ago by
LauferVA
4.8k • written 4.2 years ago by
putty
▴ 40
1
vote
1
reply
888
views
Cell cycle gene list for Rat
RNA
Seurat
rat
sequencing
10x
updated 4.1 years ago by
ATpoint
89k • written 4.1 years ago by
Lauren
• 0
5
votes
4
replies
3.3k
views
fgsea returns empty dataframe
GSEA
NMF
R
fgsea
gene-expression
4.1 years ago by
charlielonergan
▴ 20
0
votes
3
replies
1.2k
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 4.1 years ago by
andres.firrincieli
3.9k • written 4.1 years ago by
bioAddict
• 0
0
votes
0
replies
752
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
4.1 years ago by
bioAddict
• 0
0
votes
0
replies
656
views
No significant gene sets in gene set enrichment analysis using the R package iDEA
gse
iDEA
mouse
4.1 years ago by
Stevens
▴ 30
1
vote
0
replies
647
views
Expression Profiling by array in Geo Datasets (Normalization)
Profiling
Expression
updated 2.8 years ago by
Ram
45k • written 4.1 years ago by
David
▴ 30
0
votes
0
replies
1.5k
views
Job:
Postdocs @ New York City: Long Reads Epigenomics, Metagenomics and Transcriptomics
epigenomics
splicing
assembly
sequencing
microbiome
4.1 years ago by
fanggang
▴ 120
1
vote
0
replies
1.9k
views
pre-imputation allele frequency check against HRC reference panel
QC
imputation
pre-imputation
TOPMed
updated 4.1 years ago by
GenoMax
153k • written 4.1 years ago by
psb7
▴ 20
6
votes
6
replies
2.7k
views
Genome-wide heterozygosity
heterozygosity
genome
3.9 years ago by
gubrins
▴ 350
1
vote
3
replies
1.3k
views
BEDtools: intersect bed on delly v0.7.8 VCF output
SV
bedtools
intersectbed
delly
VCF
4.1 years ago by
Helena
• 0
3
votes
4
replies
1.8k
views
PCA for combined set
plink
bcftools
vcf
PCA
4.1 years ago by
raalsuwaidi
▴ 110
2
votes
3
replies
1.4k
views
Description (of at least top levels) of Gene Ontology hierarchy ?
GO
4.1 years ago by
Alexander
▴ 220
5
votes
3
replies
13k
views
deseq2 replicates error
R
RNA-Seq
updated 4.1 years ago by
Nai
▴ 50 • written 5.5 years ago by
Balatheskulter
• 0
0
votes
1
reply
827
views
Viral Amplicon Haplotype Calling
gatk
freebayes
illumina
paired-end
amplicon
4.1 years ago by
geneticatt
▴ 140
1
vote
4
replies
1.6k
views
Filter bam file AND header
filter
header
BAM
4.1 years ago by
quentin54520
▴ 120
1
vote
3
replies
1.7k
views
Picard Markduplicates and samtools markdup Issues with samtools view and htseq
Markduplicates
Picard
RNASeq
samtools
updated 4.1 years ago by
Pierre Lindenbaum
166k • written 4.1 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 4.1 years ago by
swbarnes2
15k • written 6.9 years ago by
sudu87
▴ 40
4
votes
6
replies
1.9k
views
Single-End to reduce cost for Differential Expression Analysis ?
expression
single-end
differential
analysis
ngs
deg
4.1 years ago by
Evan
▴ 250
0
votes
0
replies
701
views
Job:
ELIXIR-UK FAIR Data Stewardship Training Fellowship
Fellowship
4.1 years ago by
Hannah
• 0
121,832 results • Page
610 of 2437
Recent Votes
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
Answer: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
Answer: Split chromosome into smaller fragments to save memory when build xg and gcsa in
C: DiffBind error when calling dba.count
Answer: CBioPortal: What does Mutation type: Targeted_Region means?
Answer: CBioPortal: What does Mutation type: Targeted_Region means?
Comment: how to start
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Comment: vg input and output files
by
Pierre Lindenbaum
166k
vg is a toolkit containing different tools. What are you talking about when you want to use 'input' and 'output' files.
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
Pierre Lindenbaum
166k
Thanks for the suggestion. I've got `--gres=gpu:2` in my sbatch header (so I imagine it doesn't change much things (?) ). I also suspect a…
Comment: Split chromosome into smaller fragments to save memory when build xg and gcsa in
by
李经纬
• 0
Thank you. Even if I build the XG index after some modifications, the building of gcsa failed even on a single chromosome. Even though I h…
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
Mensur Dlakic
★ 29k
For posterity, here is `nvidia-smi` output for our cluster: ``` +-------------------------------------------------------------------------…
Answer: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
Mensur Dlakic
★ 29k
How often do we get a chance to help @yokofakun after all the help Pierre has provided? I feel like we have to make a serious effort here. …
Comment: DiffBind error when calling dba.count
by
Irene
• 0
I am having the same issue with the same situation, so i do not understand what could be the problem...i do not know if you finally figure …
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
Pierre Lindenbaum
166k
@genomax I'm using the 'GPU' queue of my cluster (SLURM). The very same config was used with another parabrick subtool and I got not probl…
Comment: Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the
by
GenoMax
153k
Are you running this under a job scheduler? Is there a separate partition for the GPU's/are they accessible to the scheduler?
Comment: Learning Bioinformatics doing Projects
by
Anjali
• 0
thank you.
Comment: Statistical test of difference between two conditions and account for the batch
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ATpoint
89k
Are the batches biological replicates?
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shelkmike
★ 1.7k
If you want to save time at the cost of having a lesser understanding of how bioinformatic programs work, you may study through the BioStar…
Answer: how to start
by
shelkmike
★ 1.7k
I would recommend, in the following order:<br> 1) Go through Bioinformatics Algorithms, either as a video course or as a book, and do all e…
Comment: Perform Hierarchical Clustering in R with ggdendro Visualization
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Bastien Hervé
6.4k
For what is worth, in a previous project, I have done some tests on different hierarchical clustering methods for single cell RNAseq. I had…
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yura.grabovska
▴ 820
* Get some data - either your own or from a paper / GEO / ArrayExpress / SRA / TCGA / cBioPortal etc etc. * Look at the methods of papers…
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ATpoint
89k
"ward.D2" -- top of the pops in terms of interpretatble clusters from gene expression data in my hands, the rest is...often crytpic.
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