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21,508 results • Page
1 of 431
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0
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9
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Machine Learning Classifiers on TCGA dataset(tpm_unstrand) gene expression data set
machine
python
RNASeq
learning
10 minutes ago by
Jakpa
▴ 50
0
votes
0
replies
20
views
getTable ignores query ranges
rtracklayer
29 minutes ago by
Kyle
• 0
0
votes
1
reply
50
views
how to do a reliable single cell sequencing analysis?
singlecell
updated 52 minutes ago by
ATpoint
68k • written 6 hours ago by
apple4lee
• 0
1
vote
2
replies
47
views
a problem with getBM
and
getBM
biomart
52 minutes ago by
sanaz
• 0
1
vote
2
replies
211
views
Recommendations needed for a tool for comparative gene set enrichment analyses via a webserver
set
webserver
enrichment
gene
analyses
1 hour ago by
fuellen
▴ 20
0
votes
0
replies
38
views
mrbayes checkpoint file not starting from linux or windows after accidental closing
mrbayes
5 hours ago by
omaridris5315
• 0
0
votes
2
replies
2.0k
views
trainGlimmerHMM Error while training a genome
software error
updated 7 hours ago by
congliu37
• 0 • written 6.7 years ago by
swati.6783
▴ 10
0
votes
0
replies
72
views
maximum fastq file size in galaxy?
fastq
rna-seq
usegalaxy
12 hours ago by
demoraesdiogo2017
▴ 80
714
votes
159
replies
104k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 4 months ago by
Biostar
1.5k • written 6.1 years ago by
Istvan Albert
96k
0
votes
1
reply
125
views
translate CDS to prot formatted with nt nubers
tool
translate
updated 15 hours ago by
Pierre Lindenbaum
152k • written 16 hours ago by
vvasta
• 0
0
votes
10
replies
1.4k
views
How to translate CDS to an amino acid sequence
translation
CDS
sequencing
updated 16 hours ago by
vvasta
• 0 • written 8 months ago by
Max
• 0
0
votes
0
replies
123
views
Functional annotation results with Eggnog mapper, For a same query several COGs, several GO:....
COGs
GOs
results
Eggnog
19 hours ago by
F.Bedjou
• 0
0
votes
2
replies
162
views
How possible deadlocks are there while migrating from MYISAM to InnoDb?
dbms
updated 16 hours ago by
Pierre Lindenbaum
152k • written 20 hours ago by
jessewhite8077
• 0
0
votes
0
replies
124
views
How quality score for somatic mutations in ICGC was calculated
somatic
mutations
ICGC
20 hours ago by
caochch
• 0
0
votes
0
replies
101
views
vcf2maf - generate 1 maf for 2 vcf files
vcf2maf
sequencing
genome
WES
maf
21 hours ago by
CH1374
• 0
0
votes
1
reply
236
views
**Error: unable to open file or unable to determine types for file**
bedtools
updated 21 hours ago by
Pierre Lindenbaum
152k • written 22 hours ago by
Neel
▴ 10
14
votes
9
replies
17k
views
7 follow
Error: unable to open file or unable to determine types for file bed file
sequencing
bed
bedtools
updated 22 hours ago by
Neel
▴ 10 • written 8.0 years ago by
sebastianzeki0
▴ 190
0
votes
1
reply
1.1k
views
Anti-miRNA oligonuclotide identification
inhibition
miRNA
anti-miRNA oligonucleotide
updated 23 hours ago by
Asan Emirsale
• 0 • written 6.0 years ago by
singh.bioinfo
▴ 30
0
votes
0
replies
158
views
News:
Course - Machine Learning in R (for omics data)
Genomics
omics
MachineLearning
R
23 hours ago by
carlopecoraro2
★ 2.2k
0
votes
0
replies
136
views
Critical criteria for filtering variants by VariantFiltration
WGS
Filtration
gatk
WES
1 day ago by
Alireza
▴ 20
2
votes
1
reply
190
views
HISAT2 output direct to bam sorted
sorted
HISAT2
bam
to
output
direct
updated 1 day ago by
ATpoint
68k • written 1 day ago by
ibq.enriquepola
• 0
0
votes
0
replies
130
views
Sc-RNA seq 5’ V2 PE auto detected by CellRanger as R2 only chemistry
cellranger
5prime
PE
R2
V2
1 day ago by
ashley.fletcher2
• 0
0
votes
0
replies
112
views
transcriptomincs
assembly
transcriptome
1 day ago by
Kiran
• 0
0
votes
0
replies
92
views
transcriptome assembly, GWA, BGC
GWA
assembly
BGC
transcriptome
1 day ago by
Kiran
• 0
0
votes
0
replies
153
views
Recommended tools/packages for power and sample size estimation for microRNA gene expression and/or protein expression study?
Power
protein
miRNA
sample
analysis
size
1 day ago by
Lalaland
▴ 10
2
votes
1
reply
189
views
bgzip error 4
bgzip
error4
vcf
updated 22 hours ago by
Pierre Lindenbaum
152k • written 1 day ago by
yb
▴ 10
0
votes
1
reply
561
views
pooled-heterozygosity calculation
VCF
Population-Genetics
WGS
Selective-sweep
updated 1 day ago by
mmcui0018
• 0 • written 15 months ago by
reza
▴ 300
1
vote
0
replies
109
views
cBioportal: Mutations in the database don't appear in the portal
cbioportal
1 day ago by
Camilo Andres
▴ 20
7
votes
3
replies
347
views
Hugely different results between edgeR and DESeq2
edgeR
RNASeq
Expression
Differential
DESeq2
updated 1 day ago by
Gordon Smyth
★ 5.4k • written 3 days ago by
Gama313
▴ 100
0
votes
3
replies
165
views
Help converting .CYCHP to .txt or .csv or .vcf
cychp
updated 1 day ago by
Pierre Lindenbaum
152k • written 1 day ago by
Sarah
• 0
1
vote
6
replies
260
views
How to Calulate Allele Frequency from a VCF File?
frequency
allele
VCF
updated 11 hours ago by
Jeremy Leipzig
21k • written 1 day ago by
Emoji
• 0
0
votes
2
replies
155
views
Gviz python alternative
Gviz
Bioconductor
Biopython
python
R
updated 1 day ago by
cmdcolin
★ 2.7k • written 1 day ago by
bhumm
• 0
0
votes
0
replies
106
views
tximeta accessing gene symbols after addIds()
deseq2
symbols
tximeta
gene
1 day ago by
iddryg
• 0
5
votes
2
replies
182
views
find tandem repeats in DNA from CRAM/VCF file
repeats
CRAM
tandem
VCF
1 day ago by
anubratadas
▴ 20
0
votes
0
replies
110
views
A way to get a list of determined and undetermined indexes using illumina interop library?
python
interop
illumina
1 day ago by
fluffycowbird
• 0
0
votes
2
replies
190
views
GSEA on nonmodel organisms
GSEA
RNAseq
transcriptomics
multispecies
R
updated 1 day ago by
dariober
14k • written 1 day ago by
Lada
▴ 10
1
vote
1
reply
126
views
How to set NCBI entrez to pipe or ignore errors?
NCBI
Entrez
updated 1 day ago by
GenoMax
125k • written 1 day ago by
rijan_dhakal
• 0
1
vote
1
reply
145
views
Plotting Correlation matrix
python
matrix
R
correlation
updated 1 day ago by
LChart
1.8k • written 1 day ago by
Zhiyi
• 0
1
vote
1
reply
139
views
Aggregate gene expression
AggregateExpression
RNASeq
Seurat
expression
gene
updated 1 day ago by
jv
▴ 740 • written 1 day ago by
Anst
▴ 30
0
votes
1
reply
125
views
bwa-meth unrecognized reference name during sam_parse
EM-seq
Methyl-seq
alignment
bwa-meth
updated 1 day ago by
GenoMax
125k • written 1 day ago by
bp22
▴ 20
0
votes
0
replies
103
views
Proloc and readMSnSet
readMSnSet
proloc
1 day ago by
ciaki
• 0
2
votes
0
replies
115
views
News:
Course - Reproducibility in Bioinformatics
Bioinformatics
Reproducibility
1 day ago by
carlopecoraro2
★ 2.2k
0
votes
0
replies
99
views
Move Cytoscape "CytoscapeConfiguration" directory
cytoscape
1 day ago by
Lucy
▴ 110
0
votes
3
replies
212
views
best way to learn bash scripting
bash
coding
sequncing
updated 1 day ago by
Jeremy
▴ 740 • written 1 day ago by
rj.rezwan
• 0
1
vote
0
replies
147
views
Job:
Senior Bioinformatician - Human Genome Sequencing
bioinformatics
Bioinformatician
postdoc
genetics
statistical
1 day ago by
NDM Recruitment
▴ 10
0
votes
0
replies
126
views
Differential Peak Analysis for a specific gene using only bigWig + BED files?
differential
peak
bigwig
chip-seq
analysis
1 day ago by
Maycon
• 0
1
vote
0
replies
106
views
Meta-analysis of rare variant SAIGE-GENE output for WGS data
meta-analysis
rare
SAIGE
variant
1 day ago by
tacrolimus
▴ 100
1
vote
3
replies
179
views
Retrieve specific fasta sequences from a group of assemblies
CDS
gene
sequence
updated 1 day ago by
Matthias Zepper
2.8k • written 1 day ago by
SushiRoll
▴ 100
2
votes
1
reply
170
views
NCBI DB and Taxonomy classification
db.NCBI
taxonomic
taxonomy
updated 1 day ago by
GenoMax
125k • written 1 day ago by
Giulia.cosenza
▴ 80
0
votes
2
replies
244
views
Error: Please supply a reference FASTA/GBK/EMBL file with --reference
snippy
Prokka
updated 1 day ago by
colindaven
4.4k • written 1 day ago by
Neel
▴ 10
21,508 results • Page
1 of 431
Recent Votes
A: Using ColSums vs sizeFactors in read count normalization
Comment: a problem with getBM
C: Reorder heatmap rows in a dataset with missing values
A: Difference between GTF file with CHR and without CHR. ENSEMBL
Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
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Teacher
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ATpoint
68k
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tianshenbio
▴ 160
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maxdlf12
• 0
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Recent Replies
Answer: how to do a reliable single cell sequencing analysis?
by
ATpoint
68k
The usual approach for starters would be to follow guided and well-accepted tutorials. That would (incomplete list) be: - The Biocon…
Answer: a problem with getBM
by
sanaz
• 0
head(ensembl_ids) X baseMean log2FoldChange lfcSE stat pvalue padj 1 ENSG00000000938.13 1344.2587 2.107…
Answer: Recommendations needed for a tool for comparative gene set enrichment analyses v
by
fuellen
▴ 20
Hello and Thanks! OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared". In any case, is …
Comment: a problem with getBM
by
Mike Smith
★ 1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`. It's …
Answer: trainGlimmerHMM Error while training a genome
by
congliu37
• 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File?
by
Jeremy Leipzig
21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)?
by
Fabio Marroni
★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism
by
Rob
▴ 160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers
by
Pierre Lindenbaum
152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence
by
vvasta
• 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
by
Pierre Lindenbaum
152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
by
Pierre Lindenbaum
152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation?
by
Fabio Marroni
★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2
by
Fabio Marroni
★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file**
by
Pierre Lindenbaum
152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
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