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117,001 results • Page
1 of 2341
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Forum:
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
just now by
marineandriot
• 0
0
votes
1
reply
53
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
updated 31 minutes ago by
swbarnes2
14k • written 4 hours ago by
Ezequiel
• 0
0
votes
0
replies
13
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 32 minutes ago by
GenoMax
142k • written 48 minutes ago by
Long
• 0
0
votes
2
replies
96
views
Trimming tool
Trimmer
tool
updated 2 hours ago by
ntsopoul
▴ 60 • written 4 hours ago by
GeneC
• 0
0
votes
0
replies
32
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
3 hours ago by
kilcdincer
▴ 10
0
votes
2
replies
60
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 40 minutes ago by
LauferVA
4.2k • written 5 hours ago by
ijarne
• 0
797
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
62
views
genomic region of transcription factor
search
HOMER
motif
5 hours ago by
qudrat.nii
▴ 10
1
vote
5
replies
259
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 4 hours ago by
dthorbur
★ 2.0k • written 23 hours ago by
BATMAN
• 0
0
votes
6
replies
183
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
46 minutes ago by
hannes.bongartz
• 0
0
votes
0
replies
54
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 9 hours ago by
GenoMax
142k • written 9 hours ago by
yura.grabovska
▴ 90
4
votes
7
replies
436
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 9 hours ago by
marco.barr
▴ 130 • written 2 days ago by
diqixiaoyaoer
▴ 20
0
votes
0
replies
61
views
constructing pangenome through psvcp
psvcp
pangenome
12 hours ago by
analyst
▴ 50
1
vote
9
replies
263
views
zero TPM for many gene including housekeeping when using kallisto
RNAseq
6 hours ago by
ashkan
▴ 160
0
votes
1
reply
97
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 11 hours ago by
dthorbur
★ 2.0k • written 12 hours ago by
Umer
▴ 50
0
votes
2
replies
160
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 6 hours ago by
Zhenyu Zhang
★ 1.2k • written 22 hours ago by
Ngrin
• 0
4
votes
9
replies
399
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
9 hours ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
156
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 14 hours ago by
Pierre Lindenbaum
161k • written 20 hours ago by
melissachua90
▴ 70
0
votes
0
replies
63
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
16 hours ago by
Varsha
• 0
0
votes
1
reply
182
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 11 hours ago by
GenoMax
142k • written 19 hours ago by
huxiangyulove
• 0
0
votes
0
replies
80
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
22 hours ago by
O.rka
▴ 720
4
votes
5
replies
4.3k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 23 hours ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
257
views
Merge clusters in Seurat UMAP
seurat
umap
14 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
84
views
Use of ichor CNA
Dog
CNA
genome
1 day ago by
sainavyav22
• 0
2
votes
2
replies
197
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 1 day ago by
Ram
43k • written 1 day ago by
txema.heredia
▴ 130
1
vote
0
replies
98
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 23 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
6
votes
4
replies
270
views
Details on salmon index
Salmon
updated 9 hours ago by
Rob
6.6k • written 1 day ago by
Lorenzo
• 0
0
votes
0
replies
90
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
1 day ago by
Jsarria.EEAD
• 0
0
votes
1
reply
141
views
How can I calculate the OS of each patient?
overall-survival
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Pedro
• 0
1
vote
1
reply
149
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 1 day ago by
Ram
43k • written 1 day ago by
m90
▴ 30
0
votes
0
replies
88
views
cat-bgen fail
bgenix
updated 1 day ago by
Ram
43k • written 1 day ago by
lambard
• 0
3
votes
4
replies
270
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 7 hours ago by
Jeremy Leipzig
22k • written 1 day ago by
Ali
• 0
3
votes
3
replies
188
views
getting exon coordinates
genomics
updated 1 day ago by
Ram
43k • written 1 day ago by
Xbox_27
• 0
0
votes
4
replies
264
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 16 hours ago by
Tony
• 0 • written 2 days ago by
vk
▴ 10
1
vote
5
replies
243
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 23 hours ago by
Ram
43k • written 1 day ago by
manuelmourato25
• 0
3
votes
4
replies
353
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Pierre Lindenbaum
161k
2
votes
11
replies
650
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
14 hours ago by
egascon
• 0
1
vote
1
reply
149
views
API kegg - IndexError: list index out of range
kegg
API
updated 19 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
mirwa.zidi93
• 0
0
votes
0
replies
93
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
1 day ago by
Novogene
▴ 420
0
votes
0
replies
97
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
1 day ago by
ebertomeup
• 0
0
votes
3
replies
232
views
Sam file Header problem
Sam
Header
problem
file
updated 15 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
saifulislam99121
• 0
1
vote
4
replies
230
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 23 hours ago by
Ram
43k • written 2 days ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
558
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 1 day ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
113
views
select set of intervals that cover a genomic region
GRanges
bed
1 day ago by
ntsopoul
▴ 60
1
vote
1
reply
160
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 23 hours ago by
Ram
43k • written 1 day ago by
dwpeng
▴ 10
0
votes
1
reply
139
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 17 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Luqman
• 0
2
votes
3
replies
219
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 23 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
0
votes
3
replies
202
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
updated 6 hours ago by
andres.firrincieli
3.6k • written 2 days ago by
mavy
▴ 10
1
vote
1
reply
230
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
2 days ago by
ramiro.barrantes
• 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 2 days ago by
Ram
43k • written 3.9 years ago by
millere
• 0
117,001 results • Page
1 of 2341
Recent Votes
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Answer: How to download dbSNP153 vcf files in hg19/GRCH37 version
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
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Ezequiel
• 0
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alanh
▴ 170
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6.0k
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Recent Replies
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool
by
GenoMax
142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
Zhenyu Zhang
★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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