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807 results • Page
2 of 17
Sort: Votes
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Views
Votes
Replies
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 29 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
6
votes
4
replies
434
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
14 days ago by
Estevão
▴ 10
6
votes
3
replies
226
views
Interpretting IGV output
IGV
updated 24 days ago by
Carlo Yague
8.7k • written 24 days ago by
analyst
▴ 50
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 29 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
5
votes
7
replies
483
views
RNA seq analysis
DESeq
RNA-seq
1 day ago by
Jacek
▴ 20
5
votes
4
replies
717
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
28 days ago by
BioinfGuru
★ 1.7k
5
votes
5
replies
2.2k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq
tophat
batch-effect
cufflinks
updated 29 days ago by
Ram
43k • written 5.4 years ago by
yff
• 0
5
votes
3
replies
758
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 27 days ago by
Enrique
• 0 • written 10 months ago by
Denis
▴ 310
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 28 days ago by
Ram
43k • written 9.2 years ago by
chengzhao41
▴ 110
5
votes
3
replies
312
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 16 days ago by
Lluís R.
★ 1.2k • written 16 days ago by
이민경[학생](대학원 융합의과학과)
• 0
5
votes
5
replies
324
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 14 days ago by
atharvakarkare14
▴ 30 • written 14 days ago by
Begonia_pavonina
▴ 150
5
votes
13
replies
2.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 26 days ago by
ATpoint
82k • written 27 days ago by
BioinfGuru
★ 1.7k
5
votes
6
replies
594
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 16 days ago by
me
▴ 760 • written 17 days ago by
Mariana
▴ 40
5
votes
4
replies
711
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
23 days ago by
kirillkirilenko
▴ 40
5
votes
2
replies
345
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 17 days ago by
i.sudbery
19k • written 20 days ago by
vanbelj
▴ 40
5
votes
5
replies
307
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
9 days ago by
Chris
▴ 280
5
votes
2
replies
436
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 21 days ago by
shalespringer
▴ 10 • written 3 months ago by
Phenylananin
▴ 20
5
votes
5
replies
661
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 13 days ago by
Mbofire
• 0 • written 22 days ago by
Ming Tommy Tang
★ 3.9k
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 2 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
4
votes
2
replies
274
views
GRCh38.gmap file
gnomix
gmap
12 days ago by
lorena9132
▴ 10
4
votes
2
replies
270
views
How can I analyze normalized expression data?
DEseq2
RNA-seq
8 days ago by
mnx0723
• 0
4
votes
2
replies
1.9k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 29 days ago by
Dr.Animo
▴ 130 • written 12 months ago by
BioinfoBee
• 0
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 13 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq
batch-effect
sequencing
updated 29 days ago by
Ram
43k • written 4.7 years ago by
dmj6ab
▴ 20
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
4
votes
3
replies
438
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 19 days ago by
Arup Ghosh
3.2k • written 20 days ago by
chaco001
▴ 40
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
17 days ago by
anna
▴ 20
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 10 days ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
4
votes
1
reply
198
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
2 days ago by
J.
▴ 40
4
votes
1
reply
353
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
17 days ago by
pairedttest
▴ 10
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 16 days ago by
Andres
▴ 20 • written 9.7 years ago by
hermathena
▴ 40
4
votes
3
replies
2.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq
picard
validatesamfile
updated 7 days ago by
Pierre Lindenbaum
161k • written 7 days ago by
Lila M
★ 1.2k
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 13 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 7 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
4
votes
7
replies
397
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
3 days ago by
Chen
• 0
4
votes
6
replies
801
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 19 days ago by
dsull
★ 6.0k • written 23 days ago by
qudrat.nii
▴ 10
4
votes
5
replies
451
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
17 days ago by
analyst
▴ 50
4
votes
1
reply
254
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 10 days ago by
zx8754
11k • written 12 days ago by
Jautis
▴ 560
4
votes
2
replies
263
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 12 days ago by
Ram
43k • written 13 days ago by
carolofharvest
▴ 40
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 8 days ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 8 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
4
votes
6
replies
4.0k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 29 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
4
votes
7
replies
631
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
17 days ago by
e.r.zakiev
▴ 210
4
votes
11
replies
880
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 23 days ago by
LauferVA
4.2k • written 24 days ago by
dominickd
• 0
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 28 days ago by
Ram
43k • written 6.6 years ago by
georgewwp
▴ 30
4
votes
0
replies
157
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
17 days ago by
Biostar
2.8k
4
votes
8
replies
763
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 20 days ago by
Alex Reynolds
35k • written 21 days ago by
J
▴ 10
4
votes
2
replies
373
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 28 days ago by
Juke34
8.6k • written 28 days ago by
njornet
▴ 20
4
votes
5
replies
4.3k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 5 hours ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
4
votes
7
replies
604
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 21 days ago by
dsull
★ 6.0k • written 22 days ago by
VITALA
• 0
807 results • Page
2 of 17
Recent Votes
Comment: switch off warning in blast command line
Forward And Reverse Strand Conventions
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Answer: Details on salmon index
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 10
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test
by
Nyksubuz
▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
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by
Nyksubuz
▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem
by
saifulislam99121
• 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite
by
dario.garvan
▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
GenoMax
142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo.
by
Ram
43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
txema.heredia
▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
swbarnes2
14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
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