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1,000 results • Page
5 of 20
Sort: Rank
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Votes
Replies
0
votes
1
reply
270
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 9 days ago by
GenoMax
141k • written 9 days ago by
bioyas
▴ 10
0
votes
0
replies
208
views
Copy number variation plot
Copy-number-variation
genomics
updated 9 days ago by
Ram
43k • written 9 days ago by
Emmi
• 0
1
vote
5
replies
716
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 9 days ago by
BioinfGuru
★ 1.7k • written 11 days ago by
rrehimi
• 0
0
votes
0
replies
183
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
9 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
289
views
Could you please assist in identifying this cluster?
single-cell
updated 9 days ago by
Ram
43k • written 9 days ago by
Kazo
• 0
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by
dvelmeshev
• 0
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 9 days ago by
ATpoint
82k • written 7.2 years ago by
boymin2020
▴ 80
5
votes
13
replies
1.2k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 8 days ago by
ATpoint
82k • written 9 days ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
424
views
Plink merge errors.
cygwin64
bed
PLINK
10 days ago by
Dinmukhamed
• 0
0
votes
0
replies
202
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 9 days ago by
Ram
43k • written 10 days ago by
Dinmukhamed
• 0
0
votes
0
replies
199
views
miRDeep2: How to get the read counts
mirdeep2
10 days ago by
Atul K.
• 0
3
votes
4
replies
671
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
6 days ago by
rahu
• 0
0
votes
0
replies
203
views
Lncipedia GTF file error
Proteomics
updated 9 days ago by
Ram
43k • written 10 days ago by
atharvakarkare14
▴ 10
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 10 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
3
votes
3
replies
482
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 9 days ago by
swbarnes2
14k • written 10 days ago by
noodle
▴ 570
0
votes
2
replies
543
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
10 days ago by
航太郎
• 0
11
votes
12
replies
982
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 10 days ago by
Ram
43k • written 10 days ago by
iamsmor
• 0
0
votes
0
replies
216
views
create genewise sync file in popoolation
popoolation
updated 10 days ago by
GenoMax
141k • written 10 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
381
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
10 days ago by
Ashok
• 0
0
votes
2
replies
419
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
10 days ago by
Ashok
• 0
0
votes
0
replies
216
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 10 days ago by
Ram
43k • written 10 days ago by
samuelkalandarov2002
▴ 10
1
vote
1
reply
374
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
10 days ago by
otieno43
▴ 30
0
votes
2
replies
428
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
9 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
206
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
6 days ago by
Javier
• 0
1
vote
4
replies
691
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 10 days ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
0
votes
0
replies
181
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
10 days ago by
enferdeflame
• 0
1
vote
1
reply
421
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 8 days ago by
Gordon Smyth
★ 7.0k • written 10 days ago by
Chris
▴ 260
0
votes
0
replies
194
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 10 days ago by
Ram
43k • written 10 days ago by
carlopecoraro2
★ 2.5k
3
votes
9
replies
814
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 10 days ago by
Elisabeth Gasteiger
★ 2.4k • written 11 days ago by
Jacky
• 0
0
votes
1
reply
271
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 10 days ago by
GenoMax
141k • written 11 days ago by
predeus
★ 1.9k
0
votes
1
reply
275
views
DEseq2
RNA-seq
DESeq2
updated 10 days ago by
Ram
43k • written 11 days ago by
rrehimi
• 0
0
votes
0
replies
177
views
News:
Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo
Individual-Based-Models
Agent-Based-Models
updated 10 days ago by
Ram
43k • written 11 days ago by
carlopecoraro2
★ 2.5k
4
votes
2
replies
325
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 11 days ago by
Juke34
8.5k • written 11 days ago by
njornet
▴ 20
1
vote
0
replies
178
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
11 days ago by
Novogene
▴ 420
0
votes
1
reply
403
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 10 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
3
votes
3
replies
513
views
Korean human genome reference file
GWAS
reference
imputation
10 days ago by
SeoGyun
• 0
0
votes
0
replies
161
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 10 days ago by
Ram
43k • written 11 days ago by
bioinfo223
▴ 10
0
votes
0
replies
180
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
11 days ago by
P.
• 0
0
votes
0
replies
171
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
11 days ago by
ekirsch
• 0
1
vote
1
reply
412
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
9 days ago by
renan.igor
• 0
2
votes
1
reply
272
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 11 days ago by
Ram
43k • written 11 days ago by
anasjamshed
▴ 120
3
votes
1
reply
601
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 11 days ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
0
votes
0
replies
182
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
11 days ago by
synat.keam
▴ 100
0
votes
1
reply
274
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 11 days ago by
GenoMax
141k • written 11 days ago by
ycts
• 0
5
votes
4
replies
639
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
10 days ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
280
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 11 days ago by
LChart
3.9k • written 11 days ago by
George
▴ 10
0
votes
4
replies
588
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
10 days ago by
Kai Xin
• 0
1
vote
1
reply
228
views
Retrieve a % coverage for each transcript
RNA-seq
updated 11 days ago by
Ram
43k • written 11 days ago by
jammydodger123456
▴ 40
0
votes
1
reply
345
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 11 days ago by
Klaus S
▴ 150 • written 17 days ago by
Zeng Hao
▴ 40
0
votes
2
replies
378
views
How can I solve this error?
metal
11 days ago by
22211020193
• 0
1,000 results • Page
5 of 20
Recent Votes
A: vcf calculation of allele counts and allele number
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
which tool/software/package should I use to preprocess the rosetta-merck microarray platform raw data?
Answer: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
NGS forensics: how to know if data is fabricated
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Answer: Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mous
by
trausch
★ 1.9k
For [delly][1], we usually augment the mouse reference genome with the additional sequence, then remap and then look in the delly output fo…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
Thats very intersting! What are the features in your classifier?
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
hagl
▴ 10
Thank you very much for the response. Following your recommendation in pursuing option one by selecting highest expressions and subsequent …
Answer: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
I think it would be pertinent to use DESEq2 to perform two comparisons: the first one between the control group and condition 1, and the se…
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
Lluís R.
★ 1.2k
Many thanks for the helpful comment. Indeed, I read some of them, but I was not fully convinced and I missed the link FAQ of DESeq2. The re…
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
ATpoint
82k
Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I followed your advice and it seems that I'm getting results comparable to what I was getting before. Upon checking with `wc -l` on the ori…
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christopher medway
▴ 450
You could perform an ANOVA to test if there is a significant association between batch number and a given Principal Component
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i.sudbery
19k
Fascinating! We also use inputs when doing metagene to protect against those situations where regions up or downstream of our metagene al…
Answer: How to solve DESeq2 Error in checkFullRank(modelMatrix)?
by
i.sudbery
19k
See the section on non full rank design matrices in the DESeq2 manual. In this case your problem is that healthy and 0dpi samples are e…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
Can you clarify what you mean by "100% of reads pass cutadapt, even though 70% of reads contain adapters and get trimmed. " did you set a m…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
I don't follow your argument for distinguishing between genomic contamination and freud. A data set being bad in terms of genomic contamin…
Comment: What does it mean single base resolution in sequencing?
by
jinyu
▴ 10
Thank you for your detail and great explanation. I do need more time to understand these. And there is still something compuzzling me. For …
Answer: Is it possible to bulk download files from GEO repository?
by
atharvakarkare14
▴ 10
Try using this library [GEOparse][1] [1]: https://github.com/guma44/GEOparse
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