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1,058 results • Page
2 of 22
Sort: Votes
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Votes
Replies
8
votes
8
replies
632
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 8 days ago by
swbarnes2
14k • written 9 days ago by
Aaliya
▴ 10
8
votes
6
replies
640
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
28 days ago by
jiao
▴ 40
8
votes
16
replies
971
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 7 days ago by
bk11
★ 2.4k • written 8 weeks ago by
Sofia
• 0
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
16 days ago by
Ram
43k
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl
repeat
updated 18 days ago by
e.r.zakiev
▴ 210 • written 16 months ago by
liorglic
★ 1.4k
8
votes
10
replies
756
views
bash script
whole-genome-sequencing
updated 18 days ago by
Ram
43k • written 25 days ago by
bestone
▴ 30
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA
batch-effect
gene-expression
updated 25 days ago by
Ram
43k • written 3.5 years ago by
Gene_MMP8
▴ 240
8
votes
5
replies
5.7k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by
a.beggs
▴ 60
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression
RNA-seq
updated 24 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 16 days ago by
John Marshall
3.0k • written 24 months ago by
bioguy24
▴ 230
7
votes
7
replies
594
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein
pdb
protein-databank
updated 21 days ago by
Matthias Zepper
4.6k • written 21 days ago by
4fzcgueyp5
• 0
7
votes
8
replies
682
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 21 days ago by
spen
▴ 40 • written 24 days ago by
MBarcelo
▴ 40
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 16 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
7
votes
3
replies
2.9k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 14 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
7
votes
8
replies
693
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
29 days ago by
Riq
▴ 50
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 8 days ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
7
votes
20
replies
6.5k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 22 days ago by
e.r.zakiev
▴ 210 • written 4.3 years ago by
kevin.stachelek
▴ 80
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray
meta-analysis
DEG
batch-effect
updated 16 days ago by
Ram
43k • written 4.9 years ago by
mosesoo
▴ 30
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 16 days ago by
Ram
43k • written 3.9 years ago by
mbk0asis
▴ 690
7
votes
6
replies
531
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
12 days ago by
analyst
▴ 30
7
votes
7
replies
1.1k
views
Prediction tools summary - zero values
statistics
updated 17 days ago by
Дана
• 0 • written 6 months ago by
Lukas
▴ 50
7
votes
10
replies
2.7k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 17 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
7
votes
4
replies
1.4k
views
Is there any journal article to reference removeBatchEffect function from Limma?
batch
removebatcheffect
limma
rna-seq
batch-effect
updated 17 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation
RNA-Seq
R
updated 16 days ago by
Ram
43k • written 6.1 years ago by
mannoulag1
▴ 120
7
votes
16
replies
712
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
4 days ago by
Ruqaiya
• 0
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA
RNA-Seq
batch-effect
updated 16 days ago by
Ram
43k • written 5.1 years ago by
tujuchuanli
▴ 100
7
votes
2
replies
291
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 10 days ago by
geneontologyhelp
▴ 390 • written 11 days ago by
catherine.teyssier
• 0
7
votes
7
replies
1.5k
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 18 days ago by
Dunois
★ 2.5k • written 19 days ago by
AdviceSeeker
• 0
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 28 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 16 days ago by
jakobjung
• 0 • written 4.6 years ago by
adhirajnath14
▴ 40
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq
edgeR
DESeq2
Batch-Effect
updated 16 days ago by
Ram
43k • written 5.2 years ago by
Behram Radmanesh
▴ 40
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq
quantification
alignment
updated 17 days ago by
Ram
43k • written 5.2 years ago by
mohammedtoufiq91
▴ 250
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 16 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 25 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 16 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
6
votes
0
replies
206
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
18 days ago by
Biostar
2.7k
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 24 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 16 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
6
votes
3
replies
203
views
Interpretting IGV output
IGV
updated 11 days ago by
Carlo Yague
8.7k • written 11 days ago by
analyst
▴ 30
6
votes
8
replies
597
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 16 days ago by
dariober
14k • written 18 days ago by
manaswiniparija3
▴ 40
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics
10x
24 days ago by
firestar
★ 1.6k
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 15 days ago by
Ram
43k • written 5.0 years ago by
borkk
▴ 140
6
votes
0
replies
2.6k
views
Tool:
Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression
batch-effect
immunology
updated 15 days ago by
Ram
43k • written 7.0 years ago by
alexis.vandenbon
▴ 80
5
votes
3
replies
359
views
Problems with Nextflow to run NanoRtax Pipeline
NanoRtax
Nextflow
Nanopore
updated 29 days ago by
colindaven
6.4k • written 4 weeks ago by
kerianaleerivera
• 0
5
votes
3
replies
733
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 14 days ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 17 days ago by
Ram
43k • written 3.0 years ago by
Mat
▴ 60
5
votes
5
replies
232
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 1 day ago by
atharvakarkare14
▴ 30 • written 1 day ago by
Begonia_pavonina
▴ 150
5
votes
4
replies
681
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
9 days ago by
kirillkirilenko
▴ 40
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva
combat
batch-effect
DESeq2
updated 17 days ago by
Ram
43k • written 3.8 years ago by
svp
▴ 680
5
votes
5
replies
514
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 6 hours ago by
Mbofire
• 0 • written 8 days ago by
Ming Tommy Tang
★ 3.9k
1,058 results • Page
2 of 22
Recent Votes
Merging a large number of VCF files
A: Merging a large number of VCF files
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
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Answer: The GDC Legacy Archive is retiring soon.
by
lcordeiro
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Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome
by
chrchang523
10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file?
by
chrchang523
10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
Answer: visualize GSEA
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I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R
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swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R
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Erina
• 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
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In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
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Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme
by
e.r.zakiev
▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ
by
GenoMax
142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
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