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117,134 results • Page
4 of 2343
Sort: Rank
Rank
Views
Votes
Replies
0
votes
4
replies
359
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
6 days ago by
Bibi
• 0
1
vote
2
replies
362
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 6 days ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
0
replies
120
views
handling bio replicates for chromHMM
replicates
chromHMM
6 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
110
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
6 days ago by
DGTool
▴ 20
1
vote
1
reply
191
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 6 days ago by
ATpoint
82k • written 6 days ago by
rj.rezwan
• 0
0
votes
2
replies
336
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
6 days ago by
Ezequiel
• 0
2
votes
0
replies
198
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
6 days ago by
micah
▴ 30
0
votes
0
replies
124
views
problems in installing rDock
rDock
updated 5 days ago by
Ram
44k • written 6 days ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 6 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
734
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 6 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
2
replies
392
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 4 days ago by
finch
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
146
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 7 days ago by
Pierre Lindenbaum
162k • written 7 days ago by
Mohamed Samir
▴ 30
0
votes
0
replies
157
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
7 days ago by
Moinuddin
• 0
0
votes
1
reply
197
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 7 days ago by
ATpoint
82k • written 7 days ago by
Jacek
▴ 20
2
votes
1
reply
268
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 7 days ago by
Gordon Smyth
★ 7.2k • written 8 days ago by
marineandriot
• 0
0
votes
0
replies
157
views
How can i use ESM-1v ?
VEP
ESM-1v
8 days ago by
Meto
• 0
0
votes
0
replies
162
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 8 days ago by
GenoMax
142k • written 8 days ago by
Long
• 0
2
votes
3
replies
356
views
Trimming tool
Trimming
updated 5 days ago by
Ram
44k • written 8 days ago by
GeneC
• 0
0
votes
0
replies
154
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
8 days ago by
kilcdincer
▴ 10
0
votes
2
replies
285
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 8 days ago by
LauferVA
4.2k • written 8 days ago by
ijarne
• 0
0
votes
0
replies
175
views
genomic region of transcription factor
search
HOMER
motif
8 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
410
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 8 days ago by
dthorbur
★ 2.0k • written 9 days ago by
BATMAN
• 0
0
votes
0
replies
162
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 8 days ago by
GenoMax
142k • written 8 days ago by
yura.grabovska
▴ 90
4
votes
9
replies
667
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 4 days ago by
marco.barr
▴ 130 • written 10 days ago by
diqixiaoyaoer
▴ 20
1
vote
1
reply
219
views
constructing pangenome through psvcp
psvcp
pangenome
7 days ago by
analyst
▴ 50
1
vote
6
replies
375
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
4 days ago by
Umer
▴ 50
0
votes
4
replies
388
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 7 days ago by
txema.heredia
▴ 130 • written 9 days ago by
Ngrin
• 0
4
votes
9
replies
538
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
8 days ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
276
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 8 days ago by
Pierre Lindenbaum
162k • written 9 days ago by
melissachua90
▴ 70
0
votes
0
replies
142
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
8 days ago by
Varsha
• 0
0
votes
1
reply
472
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 8 days ago by
GenoMax
142k • written 9 days ago by
huxiangyulove
• 0
0
votes
0
replies
159
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
9 days ago by
O.rka
▴ 720
4
votes
5
replies
4.5k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 9 days ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
382
views
Merge clusters in Seurat UMAP
seurat
umap
8 days ago by
kilcdincer
▴ 10
0
votes
0
replies
164
views
Use of ichor CNA
Dog
CNA
genome
9 days ago by
sainavyav22
• 0
1
vote
0
replies
181
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 9 days ago by
Ram
44k • written 9 days ago by
carlopecoraro2
★ 2.5k
6
votes
4
replies
393
views
Details on salmon index
Salmon
updated 8 days ago by
Rob
6.6k • written 9 days ago by
Lorenzo
• 0
0
votes
0
replies
168
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
9 days ago by
Jsarria.EEAD
• 0
0
votes
2
replies
286
views
How can I calculate the OS of each patient?
overall-survival
5 days ago by
Pedro
• 0
1
vote
1
reply
237
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 9 days ago by
Ram
44k • written 9 days ago by
m90
▴ 30
0
votes
0
replies
161
views
cat-bgen fail
bgenix
updated 9 days ago by
Ram
44k • written 9 days ago by
lambard
• 0
3
votes
4
replies
370
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 8 days ago by
Jeremy Leipzig
22k • written 9 days ago by
Ali
• 0
3
votes
3
replies
272
views
getting exon coordinates
genomics
updated 9 days ago by
Ram
44k • written 9 days ago by
Xbox_27
• 0
0
votes
4
replies
365
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 8 days ago by
Tony
• 0 • written 10 days ago by
vk
▴ 10
1
vote
5
replies
359
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 9 days ago by
Ram
44k • written 9 days ago by
manuelmourato25
• 0
3
votes
4
replies
450
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 9 days ago by
GenoMax
142k • written 9 days ago by
Pierre Lindenbaum
162k
2
votes
11
replies
805
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
8 days ago by
egascon
• 0
1
vote
1
reply
217
views
API kegg - IndexError: list index out of range
kegg
API
updated 9 days ago by
Nyksubuz
▴ 20 • written 9 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
157
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
9 days ago by
Novogene
▴ 420
0
votes
0
replies
153
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
9 days ago by
ebertomeup
• 0
117,134 results • Page
4 of 2343
Recent Votes
Low DESeq2 Sensivity on scRNA Pseudobulk Samples
DESEQ2: How can I convert ensembl gene id's to HGNC gene names.
Problem with Ensembl version identifiers after running DESeq2
Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
A: Looking for differential gene expression between treatment, within a specific cl
How to compare cell-type ratios in sc-RNA seq data?
How to calculate cell type frequency between two groups in single cell data
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Recent Replies
Comment: Merging multiple samples in Seurat
by
Picasa
▴ 640
did you split by sample or donor ?
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
That is correct
Answer: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
ATpoint
82k
That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
Comment: Error when i use EVidenceModeler to do the genome annotation
by
peanut
• 0
thank you so much ,i get it
Comment: Number of non-ATCG nucleotides replaced by Salmon
by
Tonya S.
▴ 10
Oops, yes, that must be where they are coming from. For some reason, I was thinking the genome was just soft-masked. How embarrassing! Than…
Answer: Number of non-ATCG nucleotides replaced by Salmon
by
Rob
6.6k
If there are no other signs that anything is awry, I probably wouldn't worry about this. Is it possible that these non-canonical nucleotid…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
I examined nine 10B runs and five 25B runs (we just started getting 25B flowcells a few months ago). I did not pay close attention but it …
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
GenoMax
142k
> I don't know how widespread these issues are outside of JGI. Very few small/medium sequencing centers likely have NovaSeq X. This is the…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
Supporting figures, taken from some slides I prepared for internal use. HDist 0, 1, and 2 correspond to 0, 1, and 2 mismatches allowed in …
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
This works. Thank you so so much!
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
• 0
I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Sara
▴ 30
Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
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