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90,529 results • Page
1 of 1811
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making a PCA from MASH distance result
MASH
R
PCA
just now by
v.berriosfarias
▴ 10
0
votes
0
replies
17
views
Query on miRDeep2
mirDeep2
mapper
2 hours ago by
mithu18mohan
• 0
2
votes
2
replies
56
views
Negative values in Cox regression analysis
survival
CoxPH
coxregression
2 hours ago by
Mran
▴ 10
0
votes
1
reply
55
views
Bam file metrics
ngs
bam
gatk
updated 6 hours ago by
GenoMax
99k • written 9 hours ago by
Sabeen
• 0
0
votes
2
replies
96
views
bedtool closest
bedtool
updated 2 hours ago by
Alex Reynolds
32k • written 19 hours ago by
CHINMAYA
• 0
583
votes
155
replies
64k
views
89 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
handbook
tutorial
training
News
updated 7 days ago by
Biostar
10 • written 4.4 years ago by
Istvan Albert
87k
2
votes
3
replies
169
views
Visualize DNA sequence as a dot plot?
plot
visualization
DNA
dot
updated 10 hours ago by
Alex Reynolds
32k • written 4 days ago by
jaydu
• 0
0
votes
0
replies
33
views
How should we replace NAs from a genelight object?
R
glpca
adegenet
GBS
SNP
10 hours ago by
jaafari.omid
▴ 50
0
votes
1
reply
65
views
To create amino acid substitution in protein structure
protein
bioinformatics
software
updated 13 hours ago by
Mensur Dlakic
★ 10k • written 19 hours ago by
shwetamgr1
• 0
0
votes
1
reply
66
views
Protein-Protein interaction for Upregulated genes
STRING
DEGs
PPI
updated 13 hours ago by
Mensur Dlakic
★ 10k • written 15 hours ago by
1961012
• 0
3
votes
8
replies
191
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq
DESeq2
updated 5 hours ago by
Ram
32k • written 14 hours ago by
sumitguptabt
▴ 10
0
votes
2
replies
75
views
Geno Ontology Analysis
GO
hypergtest
updated 12 hours ago by
h.mon
32k • written 15 hours ago by
1961012
• 0
1
vote
0
replies
53
views
News:
Bioinformatics Solutions on AWS
AWS
Bioinformatics
Cloud
updated 12 hours ago by
h.mon
32k • written 15 hours ago by
Jillian
▴ 10
1
vote
3
replies
153
views
How to retrieve protein sequence from gene ID and output a fasta file
ncbi
gene
protein
biopython
entrez
updated 6 hours ago by
GenoMax
99k • written 1 day ago by
minifoog
• 0
0
votes
0
replies
39
views
drug resistance informations for variations
cosmic
somatic
drug
variants
germline
20 hours ago by
enes
• 0
0
votes
1
reply
57
views
DiffBind consensus peak extraction
DiffBind
ChIP-seq
updated 16 hours ago by
Rory Stark
★ 1.0k • written 21 hours ago by
wei.zhang
• 0
1
vote
2
replies
71
views
hisat2 output from paired en reads.
hisat2
rna-seq
updated 22 hours ago by
Zhilong Jia
★ 1.7k • written 22 hours ago by
Palgrave
▴ 30
1
vote
2
replies
80
views
GATK variant annotation
vcf
gatk
updated 17 hours ago by
Ram
32k • written 22 hours ago by
shubhamkumbhar420
• 0
0
votes
0
replies
45
views
Assembly pipeline for SMRT (PacBio) sequenced bacterial genome data?
sequence
genome
perl
python
pipeline
21 hours ago by
Kumar
▴ 50
0
votes
0
replies
29
views
MACS2 Summit TSSPlot dividing BDG into bins
TSS
Callpeaks
MACS2
23 hours ago by
Seigfried
▴ 70
0
votes
0
replies
1.2k
views
Include - in part of the motif for analysis? And "It looks like we don't support this file format" when opening weblogo motif
motif
aminoacids
sequence
biopython
weblogo
23 hours ago by
minifoog
• 0
0
votes
0
replies
82
views
LD score regression of data including SNPs with extremely low P-value
heritability
SNP
LDSC
15 hours ago by
Apprentice
▴ 50
0
votes
1
reply
98
views
gRNA concatamer - will it work ?
gRNA
CRISPR
PAM
updated 22 hours ago by
ATpoint
48k • written 1 day ago by
Rajesh
• 0
0
votes
1
reply
67
views
Understanding the ColData Matrix
RNA-SEQ
R
Micheal_Love
DESEQ2
updated 1 day ago by
jared.andrews07
9.3k • written 1 day ago by
raisamathenge
▴ 10
0
votes
0
replies
104
views
Job:
Bioinformatician/Programmer at the University of Pennsylvania
pipelines
programmer
bioinformatician
python
r
1 day ago by
adamnaj
• 0
0
votes
0
replies
60
views
Job:
Bioinformatician at Turbine / Hungary
proteomics
cancerreserach
singlecell
python
r
1 day ago by
timea.volenter
• 0
0
votes
0
replies
36
views
panel of normals for mutect2
mutect2
gatk
NGS
PoN
somatic
1 day ago by
lait
▴ 160
0
votes
2
replies
86
views
format conversion using OpenBabel
software
14 hours ago by
roybatty269
• 0
0
votes
0
replies
46
views
How to compare enrichment scores?
enrichment
scores
1 day ago by
fpizzagalli
• 0
0
votes
0
replies
41
views
Should I take FDR < 0.2 for differentially abundant bacteria found in meta-analysis random effect ?
FDR
Microbiome
1 day ago by
deep771992chanda
▴ 30
0
votes
1
reply
69
views
Program for predicting RNA sequences that may bind to a protein Domain
protein
Binding
domain
RNA
updated 1 day ago by
Mensur Dlakic
★ 10k • written 1 day ago by
noahhelton98
▴ 10
2
votes
5
replies
267
views
Understanding TCGA's ASCAT copy number data
tcga
ascat
copy number
updated 1 day ago by
Zhenyu Zhang
▴ 280 • written 6 weeks ago by
loughrae
▴ 70
0
votes
1
reply
111
views
GDC Data Query
RNA-Seq
updated 1 day ago by
Zhenyu Zhang
▴ 280 • written 4 weeks ago by
p20170409
• 0
1
vote
3
replies
87
views
Redundancy reduction of de novo transcriptome assemblies with Compacta?
de-novo
transcriptome
redundancy-reduction
21 hours ago by
Dunois
▴ 620
0
votes
5
replies
137
views
Cellranger count.srun issues
cellranger
srun
updated 1 day ago by
GenoMax
99k • written 1 day ago by
gonzalezb549
• 0
1
vote
1
reply
93
views
Up-to-date GWAS Power Calculator and GWAS power comparison
GWAS
power
updated 1 day ago by
Kevin Blighe
72k • written 5 days ago by
moxu
▴ 480
1
vote
1
reply
2.3k
views
How to design WGCNA: one analysis over all sample or seperate analysis (using consensus module analysis)?
WGCNA
RNA-seq
updated 1 day ago by
Kevin Blighe
72k • written 3 days ago by
leesooyeon94
▴ 10
3
votes
2
replies
111
views
Contradiction in Harzard ratio and Log fold change
Foldchange
Cancer
HR
HarzardRatio
LogFC
10 hours ago by
Mran
▴ 10
0
votes
0
replies
45
views
Refs/tools for protein interactomes
Protein
PSI-MI
Interactome
Orthologs
PPI
1 day ago by
ian.will
• 0
0
votes
4
replies
148
views
How to plot a image like this.
plot
Bioinformatics
Cancer
R
Genome
1 day ago by
lincaijin1994
• 0
1
vote
2
replies
117
views
HaplotypeCaller VCF depth is greater than the number of reads in bam
HaplotypeCaller
vcf
gatk
1 day ago by
wang.yiguan
• 0
0
votes
1
reply
62
views
How to get Data from https://www.orthodb.org/ by the list of UniprotID
Bioinformatics
updated 1 day ago by
GenoMax
99k • written 1 day ago by
Trinh
• 0
1
vote
4
replies
110
views
samtools idxstats unplaced contigs
contig
STAR
samtools
updated 1 day ago by
Martombo
★ 2.7k • written 1 day ago by
LacquerHed
• 0
0
votes
2
replies
77
views
16S data classification using kraken and centrifuge
centrifuge
16S
classification
kraken
updated 1 day ago by
cpad0112
15k • written 1 day ago by
twinklemishra0892
• 0
0
votes
3
replies
103
views
Differential expression analysis with LIMMA results
DGE
1 day ago by
najioumayma
▴ 10
1
vote
2
replies
95
views
Is there a way to include not conda package/programs to snakemake environment?
Non-Conda_packages
Snakemake
17 hours ago by
lmlukoseviciute
▴ 20
1
vote
2
replies
88
views
How to parse all the Zn-binding protein sequences from MetalPDB?
PDB
database
NCBI
protein
python
1 day ago by
Kumar
▴ 50
0
votes
0
replies
31
views
How to assemble short DNA sequences using ABYSS?
sequence
multiple-alignment
assembly
1 day ago by
anikcropscience
▴ 40
0
votes
1
reply
50
views
How to run SPAdes assembler with bam files?
spades
assembler
bam
updated 1 day ago by
GenoMax
99k • written 1 day ago by
marongiu.luigi
▴ 560
2
votes
1
reply
59
views
Filter contig fasta file by GC content
contig
gc
updated 1 day ago by
GenoMax
99k • written 1 day ago by
victoriahristovaa
• 0
90,529 results • Page
1 of 1811
Recent Votes
Answer: differential expression analysis
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
C: The Biostar Handbook, a bioinformatics e-book for beginners
Answer: Negative values in Cox regression analysis
Answer: Negative values in Cox regression analysis
Comment: SHAPEIT2 - ERROR "BAD RECOMBINATION RATE"
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au.rinki.bio
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lakhujanivijay
5.4k
Teacher
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Recent Replies
Comment: Negative values in Cox regression analysis
by
Mran
▴ 10
Yes. I have seen your comment very useful. So thanks to you, I am now sure about my path in analysis. Thanks so much
Comment: Meaning letters in TCGA sample barcode field
by
Ram
32k
Please avoid terms like "dear". This is a formal, professional setting and these words are of a more personal/intimate nature.
Comment: single tumor vs multiple normal sample differential gene expression (RNA-Seq ) a
by
Ram
32k
> The EdgeR was also showing an error during "DGEList" and asking for minimum 3 data samples for each group so I just duplicated the single…
Comment: Using EnrichedHeatmap for visualization of NGS experiments
by
goodwinjinesh
• 0
Thank you. Yes. I have one more question. Can I create a file only with first three columns (col-1: Chr1; col-2: Start; col-3: end) and exp…
Comment: Bam file metrics
by
GenoMax
99k
`Qualimap` ([LINK][1]) would be one good option for overall metrics. You will not get all the metrics you are looking from one package. …
Comment: How to retrieve protein sequence from gene ID and output a fasta file
by
GenoMax
99k
Consider accepting the answer (green check mark) then.
Answer: Negative values in Cox regression analysis
by
Kevin Blighe
72k
Yes, you can use a dataset that comprises both positive and negative Z scores. I am assured that you understand what each value on the Z-sc…
Comment: RNAseq data analysis of pooled data
by
grant.hovhannisyan
★ 2.1k
hi, drop me an email to grant.hovhannisyan@gmail.com and I will send you the materials
Answer: bedtool closest
by
Alex Reynolds
32k
If you can use the `bedops` kit, you can use `closest-features` to solve this: 1. Separate reference and ncRNA files by strand and sort: …
Comment: Contradiction in Harzard ratio and Log fold change
by
Mran
▴ 10
Thank you so much. I think so, that some signaling pathways are involved here specially some regulators like Tumor suppressors and oncogene…
Answer: Visualize DNA sequence as a dot plot?
by
Alex Reynolds
32k
A text-based option might also be handy. Here's a Python script that uses the `sty` library: #!/usr/bin/env python ''' bi…
Comment: Meaning letters in TCGA sample barcode field
by
sumitguptabt
▴ 10
Yeah sure, dear. It was my first question and thought that it may bring immediate attention. Although latter I resolved this issue myself b…
Comment: single tumor vs multiple normal sample differential gene expression (RNA-Seq ) a
by
sumitguptabt
▴ 10
I tried EdgeR and DEseq2 however DEseq2 was showing an error during the creation of the DEseq2DataSet object from the matrix, It was only w…
Comment: bedtool closest
by
Ram
32k
Side note: It's bedtools, not "bedtool".
Comment: Meaning letters in TCGA sample barcode field
by
Ram
32k
Please don't tag individual users requesting their attention unless you're asking a question on packages they designed.
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