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117,240 results • Page
1 of 2345
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0
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11
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Indexing individual nucleotides across genome with NumPy-compatible output
nucleotide
array
genome
NumPy
indexing
1 hour ago by
Michael Gruenstaeudl
• 0
0
votes
1
reply
93
views
Retrive amino acids sequences from NCBI E-Direct
E-Direct
10 hours ago by
Patadu94
• 0
801
votes
167
replies
145k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
0
votes
0
replies
63
views
Surpsrisingly short reads in illumina 1.9 Miseq runs (2X300)
NGS
12 hours ago by
Mohamed Samir
▴ 30
0
votes
1
reply
101
views
I got qlen = 276 using bam_cigar2qlen in htslib but I count that cigar by myself, it should be 263.
bam
cigar
htslib
13 hours ago by
Aaron
▴ 10
1
vote
6
replies
376
views
Forum:
How do you make an original contribution to knowledge in applied bioinformatics?
thesis
academia
PhD
8 hours ago by
Edna
• 0
0
votes
0
replies
66
views
DEXSeq estimateDispersions - Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
18 hours ago by
Sara
▴ 30
0
votes
0
replies
77
views
Adapter contamination trimming using Cutadapt
NGS
data
preprocessing
18 hours ago by
citronxu
▴ 20
0
votes
1
reply
95
views
interpreting hisat2 alignment summary from paired end reads
hisat2
summary
updated 14 hours ago by
GenoMax
142k • written 20 hours ago by
analyst
▴ 50
0
votes
0
replies
66
views
mSVM for detecting hub genes
clustring
SMV
hub_genes
21 hours ago by
Morteza
• 0
0
votes
0
replies
90
views
Does it make sense to use scRNAseq for this experiment?
scRNA-seq
updated 1 day ago by
Ram
44k • written 1 day ago by
Mark
• 0
0
votes
6
replies
254
views
RNA Seq Paired End High Duplication Rate
fastqc
RNA-seq
FASTQ
updated 15 hours ago by
GenoMax
142k • written 1 day ago by
Tara
• 0
0
votes
2
replies
173
views
How to generate an oncoplot with most frequently mutated genes using maftools with annovar annotated output files
oncoplot
Maftools
Annovar
updated 1 day ago by
Ram
44k • written 1 day ago by
sainavyav22
• 0
0
votes
0
replies
86
views
How to compute gsea overlap of gene set with R
gsea
overlap
1 day ago by
Picasa
▴ 640
0
votes
0
replies
87
views
Can I combine several pseudobulked scRNAseq and bulk RNAseq datasets for DESeq2 analysis?
DESeq2
differential-expression
updated 1 day ago by
Ram
44k • written 1 day ago by
aquamarine
• 0
0
votes
1
reply
125
views
How to cluster microbial samples after principal coordinate analysis based on beta-diversity
clustering
bray-curtis
microbiome
pcoa
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
Bertalan_Takacs
▴ 100
0
votes
0
replies
94
views
How to get the sample matrix programmatically, TCGA
R
cBioPortal
Python
TCGA
1 day ago by
pcomps49
• 0
2
votes
2
replies
173
views
Filtering VCF - minimal valid filter parametrs
vcf
19 hours ago by
Lukas
▴ 50
0
votes
9
replies
334
views
Forum:
Posts getting removed?
meta
biostars
1 day ago by
noodle
▴ 590
0
votes
1
reply
110
views
gProfiler vs Panther_go in overrepresentation pathways R analysis
pathways
Reactome
Panther
Overrepresentation
gProfiler
updated 1 day ago by
GenoMax
142k • written 1 day ago by
tchosange
• 0
2
votes
3
replies
181
views
Pseudobulking per patient
scRNA-seq
Seurat
Pseudobulk
updated 1 day ago by
jared.andrews07
★ 17k • written 1 day ago by
bio_info
▴ 20
0
votes
1
reply
225
views
Combining VG graphs
vg
updated 1 day ago by
Ram
44k • written 7 weeks ago by
AshleeThomson
▴ 90
4
votes
2
replies
309
views
NCBI CLI Download all proteins from Taxid
ncbi
updated 1 day ago by
MirianT_NCBI
▴ 730 • written 8 weeks ago by
dthorbur
★ 2.0k
0
votes
0
replies
102
views
Clusters in Differential Gene Expression Data
gdc
gene-expression
seurat
updated 1 day ago by
Ram
44k • written 1 day ago by
Scofield
• 0
0
votes
1
reply
119
views
Single cell - integration after demultiplexing samples?
integration
demultiplexing
single-cell
updated 1 day ago by
bk11
★ 2.5k • written 1 day ago by
txema.heredia
▴ 130
0
votes
0
replies
100
views
Polyphen-2 for non-human organisms
polyphen-2
1 day ago by
Vitis
★ 2.5k
1
vote
4
replies
185
views
Retrieving oxyanion hole residues positions from UniProt or PDB databases
Oxyanion
Proteins
PDB
Uniprot
Hole
updated 1 day ago by
Elisabeth Gasteiger
★ 2.4k • written 1 day ago by
Mariana
▴ 50
0
votes
0
replies
98
views
Using CNVkit for checking normal samples
CNV
cnvkit
1 day ago by
DGTool
▴ 30
0
votes
0
replies
103
views
How to count number of haplotypes and haplotype frequency from phased vcf files?
haplotypes
1 day ago by
RAJAONARIVELO
• 0
4
votes
11
replies
306
views
6 follow
Asking for parallel jobs setting on HPC when analyzing sequencing data
HPC
parallel
updated 1 day ago by
Darked89
4.6k • written 1 day ago by
QX
▴ 10
0
votes
2
replies
155
views
Is there a common acceptance criteria for sample contamination?
contamination
updated 1 day ago by
jared.andrews07
★ 17k • written 1 day ago by
CY
▴ 750
0
votes
0
replies
86
views
monolce3 object: change groups naming
R
monocle3
1 day ago by
sooni
▴ 20
5
votes
1
reply
168
views
Forum:
Mailing list for academic programs and positions
masters
phd
updated 1 day ago by
Ram
44k • written 2 days ago by
Eren
• 0
0
votes
2
replies
205
views
Batch correction prior to running DESEQ2
R
RNA-seq
DESEQ2
DGE
transcriptomics
updated 1 day ago by
Ram
44k • written 2 days ago by
jayju
• 0
2
votes
2
replies
206
views
News:
Online - Autumn School in Bioinformatics
Singularity
NGS
Phylogenomics
RNA-seq
Docker
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
119
views
DMRs on subset of genes methylation array data
DMR
DMRs
methylation
EPIC
2 days ago by
kaaz
• 0
0
votes
1
reply
145
views
Add Subscripts to labels in Seurat DimPlot
DimPlot
ggplot2
Seurat
RStudio
updated 2 days ago by
bk11
★ 2.5k • written 2 days ago by
Saran
▴ 50
4
votes
11
replies
537
views
RNA-seq differentially expressed genes (DEGs) with low fold change values
ComBat-seq
RNA-seq
DESeq2
DEGs
updated 1 day ago by
swbarnes2
14k • written 3 days ago by
singlecell_bio
• 0
0
votes
3
replies
212
views
find DEG of monocle 3 object using tradeSeq
tradeSeq
updated 2 days ago by
Ram
44k • written 2 days ago by
synat.keam
▴ 100
0
votes
3
replies
427
views
Are there different ways of calculating log2FC?/How do I manually calculate gene log2FCs for continuous variables?
scRNA-seq
updated 1 day ago by
ATpoint
83k • written 2 days ago by
j.parker1993
• 0
0
votes
3
replies
227
views
QC filtering for 10x Single Cell Gene Expression Flex Fixed RNA Profiling
10x
Seurat
scRNA-Seq
1 day ago by
yura.grabovska
▴ 90
0
votes
2
replies
211
views
RNA seq
Deseq2
updated 2 days ago by
Ram
44k • written 2 days ago by
Sudip
• 0
0
votes
1
reply
178
views
InferCNV results interpretation
CNV
inferCNV
scRNA-seq
updated 2 days ago by
jared.andrews07
★ 17k • written 3 days ago by
Yingying
• 0
1
vote
2
replies
194
views
Combining microarray, RNA Seq, whole & exome sequencing
Microarray
RNA
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Bine
▴ 60
9
votes
6
replies
521
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq
padj
p-value
1 day ago by
May Ling
▴ 10
1
vote
1
reply
133
views
Alternative Database for Somatic Indel Realignment (COSMIC Alternative)
COSMIC
updated 2 days ago by
DGTool
▴ 30 • written 2 days ago by
ManuelDB
▴ 80
0
votes
2
replies
201
views
Minimap2 chimeric reads
minimap2
chimeric-reads
updated 2 days ago by
cmdcolin
★ 3.8k • written 2 days ago by
Fadwa
▴ 10
0
votes
7
replies
305
views
small RNA-seq length distribution of 100nt?
small-rnaseq
fastp
mirnas
updated 1 day ago by
GenoMax
142k • written 2 days ago by
karlaarz
▴ 110
0
votes
1
reply
169
views
Exome sequencing dataset for SKAT
SKAT
VEP
exome-sequencing
updated 2 days ago by
Pierre Lindenbaum
162k • written 3 days ago by
aurina.arnatk
▴ 10
0
votes
0
replies
122
views
Estimate/calculate power for two-sample Mendelian randomization?
MR
2 days ago by
huynguyenacademia
• 0
117,240 results • Page
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Why some microarray data have negative value? How to fix it?
A: Why some microarray data have negative value? How to fix it?
C: Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:None
Comment: Pseudobulking per patient
Answer: Mailing list for academic programs and positions
A: Nextflow using existing Conda Environments
Answer: DESeq2 model matrix not full rank
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Comment: How do you make an original contribution to knowledge in applied bioinformatics?
by
Edna
• 0
Thank you, this was really helpful and clarifying for me. While I couldn't find anybody comfortable mentoring me in bioinformatics in the b…
Comment: Retrive amino acids sequences from NCBI E-Direct
by
Patadu94
• 0
I found this old [post][1] and I was able to retrive a single amino acid sequence for the Gene_ID (Locus_Tag) that I include in the `-query…
Comment: I got qlen = 276 using bam_cigar2qlen in htslib but I count that cigar by myself
by
Aaron
▴ 10
my encoding logic is as following: const static std::unordered_map<int, int> opMapping { {'M', 0}, {'I', 1}, {'D', 2}, …
Comment: interpreting hisat2 alignment summary from paired end reads
by
GenoMax
142k
30821396 (82.71%) aligned concordantly exactly 1 time --> Uniquely mapped 2329205 (6.25%) aligned concordantly >1 times --> Multi-mapped
Answer: How do you make an original contribution to knowledge in applied bioinformatics?
by
i.sudbery
19k
If we modify the question to be "How do we make a contribution in applied molecular biology?" we would think this was a very odd question. …
Comment: Set the same Y scale for different plots
by
G.S
▴ 10
Thanks very much for your help! This code works and solves the problem. I really appreciate you going the extra mile and adding a code expl…
Comment: Filtering VCF - minimal valid filter parametrs
by
Lukas
▴ 50
Thank you so much. I think this is literally what i was looking for. You are lifesaver.
Comment: How to calculate cell type frequency between two groups in single cell data
by
Francesco
▴ 20
For me scProportionTest library does the trick.
Answer: How do you make an original contribution to knowledge in applied bioinformatics?
by
noodle
▴ 590
I'm 10 years in the field of 'molecular biology', which could be considered early-mid career. My opinion is that these days you need profic…
Comment: RNA Seq Paired End High Duplication Rate
by
Tara
• 0
Thank you! repair.sh worked great!
Comment: Posts getting removed?
by
noodle
▴ 590
> Was this example your post or a post you had posted in? I don't recall. It's only for an example here as I noticed that it was deleted a…
Comment: Posts getting removed?
by
GenoMax
142k
I am going to tag https://www.biostars.org/u/2/ (site owner) since he is the only person who has the means of tracking things on database e…
Comment: Posts getting removed?
by
noodle
▴ 590
> Give us examples. It's hard to search deleted posts. Was this one removed by mods or the user (possibly me)? https://www.biostars.org/p…
Comment: Posts getting removed?
by
Ram
44k
> users should be forced to educate themselves before being allowed to post How I wish this could be enforced - we used to have a mechanis…
Comment: Posts getting removed?
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Mensur Dlakic
★ 27k
> I've written a few how-to posts that are aimed to educate users. New users rarely invest time in reading before creating a new post so th…
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